Fungal cells and fermentation processes

ABSTRACT

The present invention provides an isolated fungal cell that is capable of producing one or more biomass-degrading enzymes and that exhibits increased or decreased expression or copy number of a polynucleotide encoding a PtaB-like protein. Also provided is a fermentation processes for producing one or more biomass-degrading enzymes comprising a fungal cells exhibiting increased or decreased expression or copy number of a polynucleotide encoding a PtaB-like protein. The biomass-degrading enzymes produced by the isolate fungal cell and fermentation processes of the present invention may be used in a process to produce soluble sugars from biomass.

RELATED APPLICATIONS

This application is a national phase of PCT/CA2012/050891 filed Dec. 12, 2012 which in turn claims the benefit of priority from U.S. Provisional Patent Application No. 61/570,545 filed Dec. 14, 2011, the content of which is hereby incorporated by reference herein in its entirety.

FIELD OF THE INVENTION

The present invention relates to fungal cells and fermentation processes for the production of biomass-degrading enzymes.

BACKGROUND OF THE INVENTION

Filamentous fungi are used for the production of enzymes and proteins for a variety of industrial biotechnology applications. Of the fungi used for enzyme production, strains of Trichoderma reesei (the asexual anamorph of Hypocrea jecorina) are particularly prominent due to their ability to secret large amounts (>50 g/L) of useful enzymes in industrial fermentations. Different high-productivity (and “hyperproductive”) Trichoderma strain lineages have been developed by different groups, almost all originating from QM6a, the “wild-type” environmental strain (Bailey and Nevalainen, 1981, Enzyme Microb. Technol. 3: 153; Vitikainen et al., 2010, BMC Genomics 11: 441, and references therein). Reported examples of high-productivity strains include QM9414 (Mandels and Andreotti, 1978, Process Biochemistry 13: 6), Rut-C30 (Eveleigh and Montenecourt, 1979, Adv. Appl. Microbiol. 25: 57), CL847 (Durand et al., 1988, Enzyme Microb. Technol. 10: 341) and M2C38 (U.S. Pat. No. 6,015,703). High-productivity strains are used to express both enzymes endogenous to the organism as well as heterologously expressed and secreted proteins. Such enzymes and proteins include cellulases, hemicellulases, amylases, proteases, laccases and esterases—all of which have been expressed for commercial purposes. Efforts continue to identify factors that regulate protein productivity so that further improvements can be made (Le Crom et al., 2009, P.N.A.S. USA 106: 16151).

High productivity is dependent upon multiple factors. Depending upon the particular strain, the carbon source and feed rate will determine which genes for secreted enzymes are induced and/or repressed, as well as the growth and enzyme production rates observed. The carbon source acts through transcription factors and their cognate promoters that are either activated or repressed under certain feed conditions. Expression of proteins is typically driven by promoters for the major cellulases and hemicellulases (e.g., Cel6A, Cel7A, Xyn11B) or hybrids thereof, e.g., a hybrid of the Cel7A and Xyn11B promoter regions and secretion signals (U.S. Pat. No. 6,015,703). The transcription factors that regulate these promoters have been partially identified and characterized. Once transcribed and translation is initiated, secretion depends upon the particular signal sequence and the secretion apparatus of the cell, both of which have been manipulated to improve productivity. All steps from carbon source through secretion can be manipulated to improve productivity by identifying and altering the regulatory proteins and networks that control the cascade of functions.

Cellulase and hemicellulase expression can be controlled, in part, by the choice of carbon source (Ilmén et al., 1997, Appl. Environ. Microbiol. 63: 1298; Mach and Zeilinger, 2003, Appl. Microbiol. Biotechnol. 60: 515; Schmoll and Kubicek, 2003, Acta Microbiologica et Immunologica Hungarica 50: 125; Ahamed and Vermette, 2009, Bioresources Technology 100: 5979). Typically, cellulose and beta-linked gluco-oligosaccharides (e.g., cellobiose, sophorose, gentiobiose, laminaribiose, lactose) induce expression of cellulases and their accessory enzymes (Mandels et al., 1962, J. Bacteriology 83: 400; Sternberg and Mandels, 1979, J. Bacteriology 139:761; Foreman et al., 2003, J. Biol. Chem. 278: 31988). Similarly, xylan, xylose and xylo-oligosaccharides will induce hemicellulases and their accessory enzymes (Royer and Nakas, 1990, Appl. Environ. Microbiol. 56: 2535; Zeilinger et al., 1996, J. Biol. Chem. 271: 25624). Glucose represses (hemi)cellulase expression in cells with a functioning cre1 gene (Ilmen et al., 1996, Mol. Gen. Genet. 251: 451). Nitrogen has well documented effects on cellular reproduction and morphology (Steyaert et al., 2010a, Fungal Biology 114: 179; 2010b, Microbiology 156: 2887), which in turn effects large scale production results (Ahamed and Vermette, 2009, Bioresources Technology 100: 5979). Nitrogen may also play a role in cellulase production. For example, it has been reported that cellulase production is elevated in an A. niger strain containing a constitutively activated nitrogen regulator AreA, while cellulase production is reduced in an AreA loss-of-function mutant grown in cellulose-induced cultures using ammonium as a nitrogen source (Lockinton et al., 2002, Fungal Genet. Biol. 37: 190).

Several major transcription factors have been identified that interact with the promoter regions of cellulase and hemicellulase genes and regulate their expression (Mach and Zeilinger, 2003, Appl. Microbiol. Biotechnol. 60: 515; Schmoll and Kubicek, 2003, Acta Microbiologica et Immunologica Hungarica 50:1 25; Kubicek et al., 2009, Biotechnology for Biofuels 2:19 and references therein). Cre1 (catabolite repression) mediates carbon catabolite repression and blocks cellulase expression when the cells are grown on glucose and other non-inducing carbohydrates (Ilmen et al., 1996, Mol. Gen. Genet. 251: 451). The gene for Cre1 is often defective or deleted in high-productivity strains (Seidl et al., 2008, BMC Genomics 9:327; Nakari-Setälä et al., 2009, Appl. Environ. Microbiol. 75: 4853). However, recent data suggest that Cre1 may also have a role in upregulation by other factors involved in cellulase and hemicellulase expression (Portnoy et al., 2011, Eukaryotic Cell 10: 262). Xyr1 (xylanase regulator) is an essential transcriptional activator that promotes expression of cellulases and hemicellulases (Stricker et al., 2006, Eukaryotic Cell 5: 2128; Stricker et al., 2007, FEBS Letters 581: 3915; Stricker et al., 2008, Appl. Microbiol. Biotechnol. 78: 211). Ace1 (activator of cellulase expression) has been identified as a repressor of cellulases and xylanases (Aro et al., 2003, Appl. Environ. Microbiol. 69: 56). Ace2, in contrast, appears to be an activator of cellulase expression under certain conditions (Aro et al., 2001, J. Biol. Chem. 276: 24309). The Hap complex (heme activator protein, named after homologous proteins originally identified in Saccharomyces cerevisiae) has been shown to interact with regulatory regions in cellulase promoters that are necessary for expression (Zeilinger et al., 2001, Mol. Genet. Genom. 266:56). Strains of Trichoderma have been isolated that cannot be induced to produce cellulases at more than basal levels, presumably due to defects in one or more of these global regulators of cellulase expression (Nevalainen and Palva, 1978, Appl. Environ. Microbiol. 35: 11; Torigoi et al., 1996, Gene 173: 199).

While feed choice and the transcription factors associated with induction and repression will determine the levels of particular mRNAs transcribed, the feed rate and secretory capacity of a particular strain will determine how much carbon in the feed goes to secreted protein versus diversion into biomass, and how much and how long protein can be secreted from the cell before feedback signals cause secretion rates to diminish. Increasing feed rate will increase protein productivity up to a point past which productivity will decrease precipitously and feed will go primarily to making biomass (Pakula et al., 2005, Microbiology 151: 135). Strains fermented under conditions leading to high productivity may be limited by the capacity of the secretory pathway. Fungal cells respond naturally by increasing expression of secretory pathway components (Saloheimo et al., 1999, Mol. Gen. Genet. 262: 35; 2004, Appl. Environ. Microbiol. 70: 459). Improvement of secretion can be achieved by intentionally over-expressing genes involved in the secretory pathway (Kruszewska et al., 1999, Appl. Environ. Microbiol. 65: 2382; 2008, Acta Biochimica Polonica 55:447). Ultimately, secretion stress can result in misfolding of proteins in the secretory pathway which will activate the unfolded protein response (UPR) and in turn down-regulate the expression of secreted proteins (Saloheimo et al., 2003, Molecular Microbiology 47: 1149; Valkonen et al., 2004, Mol. Genet. Genom. 272:443). An additional response in Trichoderma—repression under secretion stress (RESS)—further down-regulates expression of secreted proteins (Pakula et al., 2003, Mol. Genet. Genom. 272:443).

Trichoderma isolates resulting from mutagenesis that are unable to produce cellulases have been reported in the literature. Torigoi et al. (1996) have previously characterized four cellulase deficient Trichoderma mutants (QM9136, QM9977, QM9978 and QM9979) obtained by UV irradiation of QM6a (Mandels et al., 1971). All of the described mutants fail produce detectable cel5A, cel6A, cel7A and cel7B transcripts when induced with sophorose or cellulose. Failure to produce cellulase in one of these mutants (QM9979) was linked to its inability to uptake cellulase di-saccharide inducer, and postulated through functional analysis to carry a defective/mutated β-glycoside permease (Kubicek et al., 1993). Still, identity of the specific gene involved and nature of mutation involved was not described

The present invention is based on the identification of a gene encoding a polypeptide involved in moderating the development of a heritable cellulase deficient phenotype that arises after prolonged fermentation of filamentous fungi. The identified gene also regulates the ability of the fungi to tolerate aggressive fermentation conditions that enable high productivity. Disclosed herein is a means for modifying or tailoring fungal cells to meet the specific requirements of different enzyme production conditions by decreasing or increasing the expression of the gene.

SUMMARY OF THE INVENTION

The present invention relates to fungal cells and fermentation processes for the production of biomass-degrading enzymes.

In a first aspect, the present invention provides an isolated fungal cell capable of producing one or more biomass-degrading enzyme and comprising an increase in copy number or expression of a polynucleotide encoding a polypeptide exhibiting from about 40% to 100% identity to SEQ ID NO: 1 or from about 50% to about 100% identity to the amino acid sequence of SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, or SEQ ID NO: 14, relative to a parental fungal cell from which the isolated fungal cell is derived.

In one embodiment, the fungal cell comprises an increase in copy number or expression, relative to a parental fungal cell from which the isolated fungal cell is derived, of a polynucleotide that hybridizes under at least high stringency conditions to any one of (i) the polypeptide coding sequence of SEQ ID NO: 2, (ii) a genomic DNA sequence comprising the polypeptide coding sequence of SEQ ID NO: 2, and (iii) a full-length complementary strand of (i) or ii), wherein high stringency conditions are prehybridization and hybridization at 42° C. for 12 to 24 hours in 5×SSPE, 0.3% SDS, 200 ng/mL sheared and denatured salmon sperm DNA, and 50% formamide followed by post-hybridization washes of three times each for 15 minutes using 2×SSC, 0.2% SDS at 65° C.

In another embodiment, the fungal cell is a species of Trichoderma, Hypocrea, Aspergillus, Fusarium, Penicillium, Neurospora, Chaetomium, Acremonium, Glomerella, Myceliophthora, Sporotrichum, Thielavia, Chrysosporium, Corynascus, Ctenomyces, Verticillium, Cordyceps, Nectria, or Magnaporthe. For example, the fungal cell may be T. reesei, H. jecorina, A. niger, A. fumigatus, A. orzyae, A. nidulans, F. oxysporum, N. crassa, C. thermophilum, A. thermophilum, G. graminicola, M. thermophila, S. thermophile, T. terrestris, T. heterothallica, C. thermophile, V. dahlia, C. militaris, N. heamatococca, or M. orzyae.

In another aspect, the present invention provides a fermentation process for the production of one or more biomass-degrading enzyme comprising providing the isolated fungal cell as described above, culturing the isolated fungal cell in a submerged liquid fed-batch or continuous culture; and providing the fed-batch or continuous culture with a feed solution comprising a carbon source. Such fermentation process results in a population of fungal cells with a 50% reduction in cel-phenotype relative to an equivalent process utilizing a parental fungal cell.

In one embodiment, the fermentation process as described above is characterized by at least a 50% increase in sustained productivity relative to an equivalent process utilizing a parental fungal cell from which the isolated fungal cell is derived

In a third aspect, the present invention relates to an isolated fungal cell capable of producing one or more biomass-degrading enzyme, comprising a decrease in copy number or expression, relative to a parental fungal cell from which the isolated fungal cell is derived, of a polynucleotide encoding a polypeptide exhibiting from about 40% to 100% identity to SEQ ID NO: 1 or from about 50% to about 100% identity to the amino acid sequence of SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, or SEQ ID NO: 14.

In one embodiment, the fungal cell comprises a decrease in copy number or expression, relative to a parental fungal cell from which the isolated fungal cell is derived, of a polynucleotide that hybridizes under at least high stringency conditions to any one of (i) the polypeptide coding sequence of SEQ ID NO: 2, (ii) a genomic DNA sequence comprising the polypeptide coding sequence of SEQ ID NO: 2, and (iii) a full-length complementary strand of (i) or (ii), wherein high stringency conditions are prehybridization and hybridization at 42° C. for 12 to 24 hours in 5×SSPE, 0.3% SDS, 200 μg/mL sheared and denatured salmon sperm DNA, and 50% formamide followed by post-hybridization washes of three times each for 15 minutes using 2×SSC, 0.2% SDS at 65° C.

In another embodiment, the fungal cell is a species of Trichoderma, Hypocrea, Aspergillus, Fusarium, Penicillium, Neurospora, Chaetomium, Acremonium, Glomerella, Myceliophthora, Sporotrichum, Thielavia, Chrysosporium, Corynascus, Ctenomyces, Verticillium, Cordyceps, Nectria, or Magnaporthe. For example, the fungal cell may be T. reesei, H. jecorina, A. niger, A. fumigatus, A. orzyae, A. nidulans, F. oxysporum, N. crassa, C. thermophilum, A. thermophilum, G. graminicola, M. thermophila, S. thermophile, T. terrestris, T. heterothallica, C. thermophile, V. dahlia, C. militaris, N. heamatococca, or M. orzyae.

In a fourth aspect, the present invention provides a fermentation process for the production of one or more biomass-degrading enzyme comprising: providing the isolated fungal cell of the third aspect; culturing the isolated fungal cell in a submerged liquid fed-batch or continuous culture; and providing the fed-batch or continuous culture with a feed solution comprising a carbon source. Such fermentation process exhibits at least about a 50% increase in maximal specific productivity (q_(p)) relative to an equivalent process utilizing a parental fungal cell. In one embodiment of this fermentation process, the feed solution is provided at a carbon addition rate is at least 0.4 grams carbon per liter per hour. In another embodiment, the feed solution is provided at a carbon addition rate is at least 0.8 grams carbon per liter per hour.

In yet another embodiment of either of the fermentation processes described above, the carbon source in the feed solution provided during the step of culturing consists of one or more cellulase-inducing carbohydrate (such as cellulose, lactose, cellobiose, sophorose, gentiobiose, and a combination thereof), one or more hemicellulose-derived carbohydrate (such as xylan, arabinoxylan, xylo-oligosaccharides, arabinoxylo-oligosaccharides, D-xylose, xylobiose, L-arabinose, D-mannose D-galactose and combinations thereof), one or more non-inducing carbohydrate (such as glucose, dextrose, sucrose, molasses, fructose, and any combination thereof); a mixture of cellulase-inducing and hemicellulose-derived carbohydrates, a mixture of cellulase-inducing and non-inducing carbohydrate, a mixture of hemicellulose-derived and non-inducing, carbohydrates, or a mixture of cellulase-inducing, hemicellulose-derived, and non-inducing carbohydrates.

The isolated fungal cells and fermentation processes of the present invention produce one or more biomass-degrading enzymes. In some embodiments, the one or more biomass-degrading enzyme is selected from the group consisting of a cellulase, a cellobiohydrolase, an endoglucanase, a beta-glucosidase, a cellulase-enhancing protein, a xylanase, a beta-xylosidase, an alpha-arabinofuranosidase, a beta-mannanase, an alpha-glucuronidase, an acetyl xylan esterase, a ferulic acid esterase, a lignin-degrading enzyme, and any combinations thereof.

In some embodiments, at least one of the one or more biomass-degrading enzymes is endogenous to the fungal cell. In other embodiments, at least one of the one or more biomass-degrading enzymes is heterologous to the fungal cell.

In a final aspect, the present invention provides a process for treating a biomass substrate with the biomass-degrading enzyme(s) produced by the fermentation processes or isolated fungal cells as describe hereinabove. In some embodiments, the biomass substrate is a lignocellulosic feedstock.

DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a map of the pJET-ptaB-delta-ura3 vector used to delete the ptaB gene from isolated T. reesei cells. PptaB—ptaB promoter and 5′ flank sequences; TptaB—ptaB terminator and 3′ flank sequences; ura3—fungal selection marker cassette encoding T. reesei orotidine-5′-monophosphate decarboxylase; AmpR—resistance to ampicillin conferring bacterial selection marker; rep(pMB1)—replication origin; pLacUV5—LacUV5 promoter.

FIG. 2 depicts the PCR verification of deletion of the ptaB gene from T. reesei transformants A—Agarose gel of PCR amplification products using ptaB promoter and terminator specific primers and genomic DNA isolated from parental M2C38aux strain (lane 2) and putative PtaB deletion strains (lanes 4-10). Lane 3 was left empty. DNA size markers (Fermentas 1 kb plus ladder) were loaded on lane 1. The size of each DNA marker fragment is indicated on the left. The bands corresponding to the fragments with expected size for ptaB deletion are shown with black arrow on the right. B—Scheme of genomic ptaB locus in strains containing ptaB deletion (top) and intact ptaB locus (bottom). PptaB—ptaB promoter and 5′ flanking sequences, TptaB—ptaB terminator and 3′ flanking sequences, ptaB—PtaB protein coding sequence, ura3—fungal selection marker cassette encoding T. reesei orotidine-5′-monophosphate decarboxylase. Primers used for PCR amplification are indicated with line arrows at their hybridization sites; PCR products are indicated with dotted lines and size of each fragment is indicated on the top of each line.

FIG. 3 shows pilot fermentation profiles of a ptaB deletion strain (A) and its parental strain (B). Fed-batch fermentations were performed as described in Example 5 with a carbon addition rate of about 1 g of carbon per liter per hour. Accumulation of biomass (dashed lines, open symbols) and total protein (solid lines, close symbols) were measured every 24 h after fermentation start. Specific productivity (dotted lines and closed triangles) was measured as mg of secreted protein produced per gram of biomass per h.

FIG. 4 shows pilot fermentation profiles of ptaB deletion strain (A) and its parental strain (B). Fed-batch fermentations were performed as described in Example 5 with a carbon addition rate of ˜0.4 g of carbon per liter per hour. Accumulation of biomass (dotted lines, open diamonds) and total protein (solid lines, closed circles) were measured every 24 h after fermentation start. Specific productivity (dotted lines and closed triangles) was measured mg of protein produced per g of fungal cells per h.

FIG. 5 shows the accumulation of cellulase non-producing (cel-) phenotype at the end of fed-batch fermentations of ptaB deletion strain and its parental strain. Biomass samples were collected after 165 h from fermentation start. Cellulase production phenotype was assessed as described in Example 6.

FIG. 6 shows a map of pTrbxl1-ptaB-7at-ura3 vector containing ptaB overexpression cassette. Pbxl1—bxl1 promoter; Tcel7a—cel7a terminator, ptaB cds—PtaB coding sequence; Pura3, ura3 cds, Tura3—fungal selection marker cassette encoding T. reesei orotidine-5′-monophosphate decarboxylase (promoter, coding sequence and terminator, respectively); AmpR—resistance to ampicillin conferring bacterial selection marker.

FIG. 7 shows pilot fermentation profiles of a PtaB overexpression strain (A) and its parental strain (B). Fed-batch fermentations were performed as described in Example 5 at a carbon addition rate of ˜1.0 g of carbon per liter per h using a mixture of cellulase-inducing and hemicellulose-derived carbohydrates. Accumulation of biomass (dotted lines, open diamonds) and total protein (solid lines, closed circles) were measured every 24 h after fermentation start. Specific productivity (dotted lines and closed triangles) was measured as mg of protein produced per g of fungal cells per hour.

FIG. 8 shows pilot fermentation profiles of a PtaB overexpression strain (A) and its parental strain (B). Fed-batch fermentations were performed as described in Example 5 at a carbon addition rate of ˜0.4 g of carbon per liter per h using a mixture of cellulase-inducing and hemicellulose-derived carbohydrates. Accumulation of biomass (dotted lines, open diamonds) and total protein (solid lines, closed circles) were measured every 24 h after fermentation start. Specific productivity (dotted lines and closed triangles) was measured as mg of protein produced per g of fungal cells per hour.

FIG. 9 shows the accumulation of cellulase non-producing (cel-) phenotype at the end of fed-batch fermentations of PtaB-overexpressing strain and its parental strain. Biomass samples were collected after 168 h and 144 h from fermentation start for High and low CAR fermentations, respectively. Cellulase production phenotype was assessed as described in Example 6.

FIG. 10 shows an alignment of SEQ ID NO: 1 with homologous amino acid sequences from other fungal species. Overall identity is 42.77%. Identical amino acids are shown in boxes, and a consensus sequence is shown under alignment. Alignment was made using DNAman program, gap penalty 3, K-tuple 2.

FIG. 11 shows an identity matrix for the amino acid sequences of thirteen fungal PtaB-like proteins to each other.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to fungal cells and fermentation processes for the production of biomass-degrading enzymes.

More specifically, the present invention relates to isolated fungal cells that exhibit enhanced or decreased expression or activity of the polypeptide encoded by SEQ ID NO: 1 and fermentation processes utilizing the isolated fungal cells for the production of one or more biomass-degrading enzyme.

The following description is of a preferred embodiment by way of example only and without limitation to the combination of features necessary for carrying the invention into effect. The headings provided are not meant to be limiting of the various embodiments of the invention. Terms such as “comprises”, “comprising”, “comprise”, “includes”, “including” and “include” are not meant to be limiting. In addition, the use of the singular includes the plural, and “or” means “and/or” unless otherwise stated. Numeric ranges are inclusive of the numbers defining the range.

Unless otherwise defined herein, the practice of the present invention involves conventional techniques commonly used in molecular biology, fermentation, microbiology, and related fields, which are known to those of skill in the art. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, some suitable methods and materials are described. Unless otherwise defined herein, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art. Unless otherwise indicated, nucleic acids are written left to right in 5′ to 3′ orientation; amino acid sequences are written left to right in amino to carboxy orientation, respectively.

All patents and publications, including all sequences disclosed within such patents and publications, referred to herein are expressly incorporated by reference.

Isolated Fungal Cells

As used herein, an “isolated fungal cell” is a fungal cell that has been modified so as to exhibit either increased or decreased expression or copy number of a polynucleotide encoding PtaB-like protein, or increased or decreased expression of a PtaB-like protein, relative to a parental fungal cell from which it is derived.

As used herein, a “parental fungal cell” is a fungal cell which has not been modified so to exhibit either increased or decreased expression or copy number of a polynucleotide encoding PtaB-like protein, or increased or decreased expression of a PtaB-like protein. A parental fungal cell may be a “wild-type” or “native” fungal cell as found in nature without any mutations or genetic modifications or it may be a fungal cell comprising one or more genetic modifications, including but not limited to a recombinant fungal cell. For example, the parental fungal cell may comprise one or more mutation that allow for enhanced production of biomass degrading enzymes under inducing conditions or in the presence of a repressing carbohydrates such as glucose (including, for example, mutations in the cre gene) or under secretion stress (including, for example, mutations in the hac1 or ire1 genes).

The parental fungal cell may also be modified for enhanced or reduced production of one or more biomass-degrading enzymes or for reduced production of proteases. Therefore, “a parental fungal cell from which the isolated fungal cell is derived” is essentially identical to the isolated fungal cell except for the increased or decreased expression or copy number of a polynucleotide encoding PtaB-like protein, or increased or decreased expression of a PtaB-like protein”

As used herein, “a recombinant fungal cell” is a fungal cell into which one or more polynucleotides have been introduced by deliberate human intervention or “recombinant means.”

As used herein, a “genetic modification” or “mutation” includes, but is not limited to, (a) heritable changes to the sequence or structure of the fungal cell's genomic DNA resulting, for example, from random mutagenesis and selection, adaptation, or epigenetic changes and (b) genetic modification to introduce polynucleotide sequences into the fungal cell using recombinant means.

For the purposes described herein, the term “increased copy number” means at least one extra copy of at least the polypeptide coding sequence of a given gene is present in the isolated fungal cell as compared to the number of copies of the same gene in a parental fungal cell from which the isolated fungal cell is derived. For example, the isolated fungal cell may contain 1, 2, 3, 4, 5, 10, or more extra copies of at least the polypeptide coding sequence of a given gene relative to the number of copies of that same gene in the parental fungal cell. The extra copies of a given gene may be integrated into the genome of the isolated fungal cell or may be present on one or more autonomously replicating vectors or plasmids present in the isolated fungal cell.

For the purposes described herein, the term “decreased copy number” means at least one less copy of at least the polypeptide coding sequence of a given gene is present in the genome of the isolated fungal cell as compared to the copy number of the same gene present in a parental fungal cell from which the isolated fungal cell is derived.

The modulation of copy numbers of genes can be measured by one of ordinary skill in the art through well-known means, for example, comparative genomic hybridization (CGH), Southern blot hybridization, or quantitative real-time PCR (qRT-PCR) from genomic DNA.

For the purposes described herein, the term “increased expression” or “overexpression” means at least about a 1.2-fold increase in the level of transcript or polypeptide encoded by a given gene, or in the activity of the resulting polypeptide, in the isolated fungal cell as compared to that exhibited by the parental fungal cell, when grown under identical or nearly identical conditions of medium composition, temperature, pH, cell density and age of culture. For example, the level of transcript or polypeptide encoded by a given gene, or in the activity of the resulting polypeptide, in the isolated fungal cell can be increased by at least 1.3-, 1.5-, 2.0-, 2.5-, 3.0-, 4.0-, 5.0-, or 10-fold, or more, as compared to that exhibited by the parental fungal cell when grown or cultured under identical or nearly identical culture conditions.

For the purposes described herein, the term “decreased expression” means at least about a 20% decrease in the level of transcript or polypeptide encoded by a given gene, or in the activity of the resulting polypeptide, in the isolated fungal cell as compared to that exhibited by the parental fungal cell when grown under identical or nearly identical conditions of medium composition, temperature, pH, cell density and age of culture. For example, the level of transcript or polypeptide encoded by a given gene, or of the activity of the resulting polypeptide, in the isolated fungal cell may be decreased by 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount therebetween, as compared to that exhibited by the parental fungal cell when grown or cultured under essentially the same culture conditions.

The modulation of expression of genes also can be measured by one of ordinary skill in the art through analysis of selected mRNA or transcript levels by well-known means, for example, quantitative real-time PCR (qRT-PCR), Northern blot hybridization, or global gene expression profiling using cDNA or oligo array hybridization.

Increased production of a polypeptide production of a given gene can be measured, for example, with immunochemical methods such as ELISA (Van Weemen, B. K. et al. (1971) FEBS Letters 15: 232-236) with antibodies specific to the individual enzyme or by assays that specifically detect and measure the activity of the polypeptide

In at least some embodiments of the present invention, the increase or decrease in copy number or expression of a gene encoding a PtaB-like protein in the isolated fungal cell can be produced by any of various random mutagenesis and selection techniques. For example, the parental fungal cell may be subjected to irradiation or chemical mutagenesis to create a library of mutated cells, which are then screened for the desired altered phenotype or genotype. Random mutagenesis and selection techniques also include “adaptive evolution techniques” or “evolutionary engineering techniques”. As used herein, the term adaptive evolution technique refers to any method or procedure employed to influence the phenotype and genetic profile of a fungal cell or organism through the use of exposure to environmental challenges, and subsequent selection of the modified and/or isolated fungal cell with the desired altered phenotype and corresponding altered genetic profile.

As used herein, “random mutagenesis and selection” refers to the process of creating by natural or artificial means, including subjecting the fungal cell to irradiation or chemical mutagenesis, a library of mutated strains, which are then screened for a desired altered phenotype. Adaptation, also referred to as “adaptive evolution” or “evolutionary engineering”, refers to any method or procedure employed to influence the phenotype and genetic profile of a fungal cell through the use of exposure to environmental challenges, and subsequent selection of a modified fungal cell with the desired altered phenotype. “Epigenetic changes” are defined as heritable changes in chromatin structure that alter the expression of one or more genes in an organism, including but not limited to, histone methylation, histone acetylation, ubiquitination, phosphorylation or sumoylation, and DNA methylation.

In at least some embodiments of the present invention, the increase or decrease in copy number or expression of a gene encoding a PtaB-like protein in the isolated fungal cell can be produced by any one of various genetic engineering techniques or recombinant means. As used herein, a “genetic engineering technique” refers to any of several well-known techniques for the direct manipulation of an organism's genes or genome. For example, gene knockout (insertion of an inoperative DNA sequence, often replacing or interrupting the endogenous operative sequence, into an organism's chromosome), gene knock-in (insertion of a protein-coding DNA sequence into an organism's chromosome), and gene knockdown (insertion of DNA sequences that encode antisense RNA or small interfering RNA, i.e., RNA interference (RNAi)) techniques are well known in the art.

Methods for decreasing or reducing gene expression are well known and can be performed using any of a variety of methods known in the art. For example, the gene can be modified to disrupt a transcription or translation initiation sequence or to introduce a frameshift mutation in the transcript encoding the polypeptide. Other methods of reducing the gene expression include post-transcriptional RNA silencing methodologies such as antisense RNA and RNA interference (RNAi). Antisense techniques involve introducing a nucleotide sequence complementary to the transcript of a target gene such that the complementary antisense nucleotide sequence hybridizes to the target gene transcript, thus reducing or eliminating the number of transcripts available to be translated into protein. Examples of expressing an antisense RNA are shown in Ngiam et al. (2000) Appl. Environ. Microbiol. 66(2):775-82; and Zrenner et al. (1993) Planta. 190(2):247-52. RNAi methodologies include double stranded RNA (dsRNA), short hairpin RNAs (shRNAs), and small interfering RNAs (siRNAs) as known to one of skill in the art, for example, the techniques of Fire et al. (1998) Nature 391:806-11; Paddison et al. (2002) Genes Dev. 16:948-58; and Miyagishi et al. (2002) Nat. Biotechnol. 20:497-500.

Methods for decreasing or reducing the expression of a gene also include partial or complete deletion of the gene, and disruption or replacement of the promoter of the gene such that transcription of the gene is greatly reduced or even inhibited. For example, the promoter of the gene can be replaced with a weak promoter, as exemplified by U.S. Pat. No. 6,933,133. Thus, where the weak promoter is operably linked with the coding sequence of an endogenous polypeptide, transcription of that gene will be greatly reduced or even inhibited.

In some embodiments, the isolated fungal cell has been genetically modified to at least partially delete one or more gene encoding a PtaB-like protein. As used herein, a gene deletion or deletion mutation is a mutation in one or more nucleotides making up the gene is missing. Thus, a deletion is a loss or replacement of genetic material resulting in a complete or partial disruption of the sequence of the DNA making up the gene. Any number of nucleotides can be deleted, from a single base to an entire piece of a chromosome. In some embodiments, complete or near-complete deletion of the gene sequence is contemplated. For example, deletion in a gene may be a deletion of at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% of the gene.

In some embodiments, the isolated fungal cell is genetically modified to increase expression of a PtaB-like protein. The PtaB-like protein may be homologous or heterologous with respect to the fungal cell. For the purposes herein, an homologous PtaB-like protein is encoded by a polynucleotide sequence that naturally occurs in, or is isolated or derived from, the same or taxonomically equivalent taxonomic species as the fungal cell. Furthermore, as is recognized by one of skill in the art, a homologous protein may contain one or more insertions, deletions and substitutions and still be considered to be “derived from” the same species as the isolated fungal cell. Such one or more insertions, deletions and substitutions may result in increased or decreased expression or activity of the homologous PtaB-like protein. Similarly, a polynucleotide encoding a homologous PtaB-like protein may contain one or more insertions, deletions and substitutions (including substitutions that optimize codon usage without altering the sequence of the encoded protein).

A heterologous PtaB-like protein is encoded by a polynucleotide sequence that naturally occurs in, or is isolated or derived from, a different taxonomic species from the fungal cell. Furthermore, as is recognized by one of skill in the art, a heterologous PtaB-like protein may contain one or more insertions, deletions and substitutions and still be considered to be “derived from” a different taxonomic species from the isolated fungal cell. Such one or more insertions, deletions and substitutions may result in increased or decreased expression or activity of the heterologous PtaB-like protein. Similarly, a polynucleotide encoding a heterologous PtaB-like protein may contain one or more insertions, deletions and substitutions (including substitutions that optimize codon usage without altering the sequence of the encoded protein).

As used herein, in respect of polynucleotide sequences, “derived from” refers to the isolation of a target polynucleotide sequence using one or more molecular biology techniques known to those of skill in the art including, but not limited to, reverse translation of a polypeptide or amino acid sequence, cloning, sub-cloning, amplification by PCR, in vitro synthesis, and the like. Furthermore, as is recognized by one of skill in the art, a polynucleotide sequence that is derived from a target polynucleotide sequence may be modified by one or more insertions, deletions and substitutions and still be considered to be “derived from” that target nucleotide sequence. Such one or more insertions, deletions and substitutions may result in increased or decreased expression or activity of the protein of interest encoded by the polynucleotide sequence and may be located within a promoter sequence, the 5′ or 3′ untranslated regions, or within the coding region for the protein of interest.

As used herein with respect to polynucleotide sequences, “isolated” or “isolation” means altered from its natural state by virtue of separating the nucleic acid sequence from some or all of the naturally-occurring nucleic acid sequences with which it is associated in nature.

In other embodiments, the fungal cell may be genetically modified by transformation of the fungal cell with a PtaB genetic construct. As used herein, “PtaB genetic construct” refers to an isolated polynucleotide comprising elements necessary for increasing or decreasing the expression of a PtaB-like protein. These elements may include, but are not limited to, a polynucleotide sequence encoding a PtaB-like protein (coding sequence), a promoter operably linked to the coding sequence and comprising polynucleotide sequences that direct the transcription and translation of the coding sequence.

The isolated fungal cell of the present invention may further comprise one or more genetic constructs that direct the production of one or more homologous or heterologous biomass-degrading enzymes. Such constructs comprise polynucleotide elements including, but not limited to, a coding sequence for the biomass-degrading enzyme, a promoter operably linked to the coding sequence and comprising a polynucleotide sequence that directs the transcription of the coding region, and a sequence encoding a secretion signal peptide operably linked to the coding sequence, as well as targeting polynucleotide sequences that direct homologous recombination of the construct into the genome of the fungal cell. The terms “secretion signal peptide”, “secretion signal” and “signal peptide” refer to any sequence of nucleotides and/or amino acids which may participate in the secretion of the mature or precursor forms of a secreted protein. The signal sequence may be endogenous or exogenous with respect to the fungal cell. The signal sequence may be that normally associated with the protein of interest or a gene encoding another secreted protein. The signal sequence may also be a “hybrid signal sequence” containing partial sequences from two or more genes encoding secreted proteins.

As understood by one of ordinary skill in the art, the coding sequence, promoter, and/or secretion signal may be derived from the parental fungal cell, from a different organism, and/or be synthesized in vitro. For example, the promoter and secretion signal may be derived from one or more genes encoding proteins that are highly expressed and secreted when a parental fungal cell is grown in the fermentation process defined below—for example, gene(s) encoding a cellulase, beta-glucosidase, cellulase-enhancing protein, a hemicellulase, or any combination thereof. These polynucleotide elements may also be altered or engineered by replacement, substitution, addition, or elimination of one or more nucleic acids relative to a naturally-occurring polynucleotide. However, it should be understood that the practice of the present invention is not limited by the choice of promoter in the PtaB genetic construct or by the choice of promoter and secretion signal in genetic constructs expression biomass-degrading enzymes.

The genetic constructs described above may contain a selectable marker for identification of transformed host cells. The selectable marker may be present on the genetic construct or the selectable marker may be a separate isolated polynucleotide that is co-transformed with the genetic construct. Choices of selectable markers are well known to those skilled in the art and include genes (synthetic or natural) that confer to the transformed cells the ability to utilize a metabolite that is not normally metabolized by the microbe (e.g., the A. nidulans amdS gene encoding acetamidase and conferring the ability to grow on acetamide as the sole nitrogen source) or antibiotic resistance (e.g., the Escherichia coli hph gene encoding hygromycin-beta-phosphotransferanse and conferring resistance to hygromycin). Alternatively, if the fungal cell expresses little or none of a chosen marker activity, then the corresponding gene may be used as a marker. Examples of such markers include trp, pyr4, pyrG, argB, leu, and the like. The corresponding host strain would therefore have to be lacking a functional gene corresponding to the marker chosen, i.e., lacking in the expression of trp, pyr, arg, leu and the like.

A genetic construct may contain a transcriptional terminator that is functional in the fungal cell, as would be known to one of skill in the art. The transcriptional terminator may be positioned immediately downstream of a coding sequence. The practice of the invention is not constrained by the choice of transcriptional terminator that is sufficient to direct the termination of transcription in the host cell.

A genetic construct may contain additional polynucleotide sequences between the various sequence elements as described herein. These sequences, which may be natural or synthetic, may result in the addition of one or more of the amino acids to the protein encoded by the construct. The practice of the invention is not constrained by the presence of additional polynucleotide sequences between the various sequence elements of the genetic constructs present in the fungal cell.

Methods of introducing a genetic construct into a fungal cell are familiar to those skilled in the art and include, but are not limited to, calcium chloride treatment of fungal protoplasts to weaken the cell membranes, addition of polyethylene glycol to allow for fusion of cell membranes, depolarization of cell membranes by electroporation, or shooting the construct through the cell wall and membranes via microprojectile bombardment with a particle gun. The practice of the present invention is not constrained by the method of introducing the genetic constructs into the fungal cell.

In some embodiments, the isolated fungal cell may be a species of the following genera of filamentous fungi: Trichoderma, Hypocrea, Aspergillus, Fusarium, Penicillium, Neurospora, Chaetomium, Acremonium, Glomerella, Myceliophthora, Sporotrichum, Thielavia, Chrysosporium, Corynascus, Ctenomyces, Verticillium, Cordyceps, Nectria, or Magnaporthe, including anamorphs and teleomorphs thereof, as well as recognized synonymous genera. For example, the isolated fungal cell may be a strain of the following fungal species: T. reesei, H. jecorina, A. niger, A. fumigatus, A. orzyae, A. nidulans, F. oxysporum, N. crassa, C. thermophilum, A. thermophilum, G. graminicola, M. thermophila, S. thermophile, T. terrestris, T. heterothallica, C. thermophile, V. dahlia, C. militaris, N. heamatococca, or M. orzyae.

It will be understood that for the aforementioned species, the isolated fungal cell presented herein encompasses both the perfect and imperfect states, and other taxonomic equivalents, e.g., anamorphs and teleomorphs, regardless of the species name by which they are known. Further examples of taxonomic equivalents can be found, for example, in Cannon, Mycopathologica 111:75-83, 1990; Moustafa et al., Persoonia 14:173-175, 1990; Stalpers, Stud. Mycol. 24, 1984; Upadhyay et al., Mycopathologia 87:71-80, 1984; Guarro et al., Mycotaxon 23: 419-427, 1985; Awao et al., Mycotaxon 16:436-440, 1983; von Klopotek, Arch. Microbiol. 98:365-369, 1974; and Long et al., 1994, ATCC Names of Industrial Fungi, ATCC, Rockville Md. Those skilled in the art will readily recognize the identity of appropriate equivalents. Accordingly, it will be understood that, unless otherwise stated, the use of a particular genus and/or species designation in the present disclosure also refers to genera and species that are related by anamorphic or teleomorphic relationship, genera and species that are recognized as synonymous, as well as those that have been or may be reclassified into one of the claimed genera or species in the future.

PtaB-Like Proteins and PtaB Polynucleotides

As used herein, a “PtaB-like protein” (or “PtaB protein” or “PtaB”) refers to a polypeptide exhibiting from about 40% to 100% identity to the amino acid sequence of SEQ ID NO: 1 or from about 50% to about 100% identity to the amino acid sequence of SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, or SEQ ID NO: 14. For example, a Pta-B like protein may exhibit 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or 100% identity, or any % identity therebetween, to the amino acid sequence of SEQ ID NO: 1 or may exhibit 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or 100% identity, or any % identity therebetween, to the amino acid sequence of SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, or SEQ ID NO: 14.

The polypeptide of SEQ ID NO: 1 exhibits significant sequence homology to the polypeptide encoded by the Aspergillus ptaB gene (“pta” stands for “putative transcriptional activator”) identified by Conlon et al., 2001, Molecular Microbiology 40: 361). The pta genes in Aspergillus were found as fusions with areB, a gene encoding a regulator of nitrogen metabolism, in strains of Aspergillus selected for suppression of mutations in areA, the principal regulator of nitrogen metabolism in Aspergillus. The genes ptaA, ptaB and ptaC were identified as fusions with areB that enabled the suppression phenotype. As their name and history imply, the actual functions of the pta genes are unknown. Homologues in genera other than Aspergillus, such as Trichoderma and Myceliophthora, are named by comparison to the Aspergillus prototype. A listing of fungal polypeptides identified as putative PtaB homologues and their source organisms are provided in Table 1.

TABLE 1 Fungal PtaB-like proteins GenBank accession SEQ % Identity to Source Organism Number ID NO: SEQ ID NO: 1 Trichoderma reesei EGR46093.1 1 100.0 Nectria heamatococca XP_003048295.1 3 61.58 Fusarium oxysporum EGU75490.1 4 62.27 Glomerella graminocola EFQ32984.1 5 54.95 Cordyceps militaris EGX90369.1 6 35.24 Verticillium dahliae EGY22518.1 7 48.96 Thielavia terrestris AEO71320.1 8 40.07 Verticillium albo-atrum XP_003006908.1 9 43.42 Neurospora crassa XP_956246.1 10 38.02 Chaetomium thermophilum EGS23794.1 11 34.76 Magnaporthe oryzae XP_368187.1 12 39.59 Botryotinia fuckeliana CCD34135.1 13 34.63 Sporotrichum thermophile AEO61562 14 40.33

As shown in Table 1, the fungal polypeptides of SEQ ID NO: 3, 4, 5, 6, 7, 8, 9, 12 and 14 exhibit at least about 40% amino acid sequence identity to SEQ ID NO: 1. Additionally, as shown in FIG. 11, the fungal polypeptide of SEQ ID NO: 1, 3, 4, 5, 6, 7, 9, 11 or 14 may exhibit at least about 50% amino acid sequence identity to at least of one of the fungal polypeptides of SEQ ID NO: 1, 3, 4, 5, 6, 7, 9, 11 and 14 derived from another source organism.

As used herein, “identity” and “percent identity,” in the context of two or more polypeptide sequences, refers to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues that are the same (e.g., share at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80% identity, at least about 85%, at least about 90%, at least about 95%, or at least about 100% identity) over a specified region to a reference sequence, when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using a sequence comparison algorithms or by manual alignment and visual inspection.

In some embodiments, the terms “percent identity,” “% identity,” “percent identical,” and “% identical,” are used interchangeably herein to refer to the percent amino acid or polynucleotide sequence identity that is obtained by ClustalW analysis (version W 1.8 available from European Bioinformatics Institute, Cambridge, UK), counting the number of identical matches in the alignment and dividing such number of identical matches by the length of the reference sequence, and using the following ClustalW parameters to achieve slow/more accurate pairwise optimal alignments—DNA/Protein Gap Open Penalty:15/10; DNA/Protein Gap Extension Penalty:6.66/0.1; Protein weight matrix: Gonnet series; DNA weight matrix: Identity.

Two sequences are “aligned” when they are aligned for similarity scoring using a defined amino acid substitution matrix (e.g., BLOSUM62), gap existence penalty and gap extension penalty so as to arrive at the highest score possible for that pair of sequences. Amino acid substitution matrices and their use in quantifying the similarity between two sequences are well known in the art (See, e.g., Dayhoff et al., in Dayhoff [ed.], Atlas of Protein Sequence and Structure,” Vol. 5, Suppl. 3, Natl. Biomed. Res. Round., Washington D.C. [1978]; pp. 345-352; and Henikoff et al., Proc. Natl. Acad. Sci. USA, 89:10915-10919 [1992). The BLOSUM62 matrix is often used as a default scoring substitution matrix in sequence alignment protocols such as Gapped BLAST 2.0. The gap existence penalty is imposed for the introduction of a single amino acid gap in one of the aligned sequences, and the gap extension penalty is imposed for each additional empty amino acid position inserted into an already opened gap. The alignment is defined by the amino acid position of each sequence at which the alignment begins and ends, and optionally by the insertion of a gap or multiple gaps in one or both sequences so as to arrive at the highest possible score. While optimal alignment and scoring can be accomplished manually, the process is facilitated by the use of a computer-implemented alignment algorithm (e.g., gapped BLAST 2.0; See, Altschul et al., Nucleic Acids Res., 25:3389-3402 [1997], which is incorporated herein by reference), and made available to the public at the National Center for Biotechnology Information Website). Optimal alignments, including multiple alignments can be prepared using readily available programs such as PSI-BLAST (e.g, Altschul et al., supra).

In some embodiments, the isolated fungal cell comprises an increase or decrease in copy number or expression of a “PtaB-encoding polynucleotide.” As used herein, a “PtaB-encoding polynucleotide” or “PtaB polynucleotide” (as well as the terms “ptaB” and “PtaB gene”) refers to a polynucleotide that hybridizes under at least high stringency conditions to any one of (i) the polypeptide coding sequence of SEQ ID NO: 2, (ii) a genomic DNA sequence comprising the polypeptide coding sequence of SEQ ID NO: 2, and (iii) a full-length complementary strand of (i) or ii), wherein high stringency conditions are prehybridization and hybridization at 42° C. for 12 to 24 hours in 5×SSPE, 0.3% SDS, 200 μg/mL sheared and denatured salmon sperm DNA, and 50% formamide followed by post-hybridization washes of three times each for 15 minutes using 2×SSC, 0.2% SDS at 65° C.

Polynucleotides and nucleic acids “hybridize” when they associate, typically in solution, due to a variety of well-characterized physico-chemical forces such as hydrogen bonding, solvent exclusion, base stacking, and the like. As used herein, the term “stringent hybridization wash conditions” in the context of hybridization experiments, such as Southern and Northern hybridizations, are sequence dependent, and are different under different environmental parameters. An extensive guide to the hybridization of nucleic acids is found in Tijssen, 1993, Laboratory Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Acid Probes, Part I, Chapter 2 (Elsevier, New York), which is incorporated herein by reference. For polynucleotides of at least 100 nucleotides in length, low to very high stringency conditions are defined as follows: prehybridization and hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 μg/mL sheared and denatured salmon sperm DNA, and either 25% formamide for low stringencies, 35% formamide for medium and medium-high stringencies, or 50% formamide for high and very high stringencies, following standard Southern blotting procedures. For polynucleotides of at least 100 nucleotides in length, the carrier material is finally removed by washing three times each for 15 minutes using 2×SSC, 0.2% SDS 50° C. (low stringency), at 55° C. (medium stringency), at 60° C. (medium-high stringency), at 65° C. (high stringency), or at 70° C. (very high stringency).

Biomass

The terms “biomass” and “biomass substrate” encompass any suitable materials that comprise cellulose (i.e., “cellulosic biomass,” “cellulosic feedstock,” and “cellulosic substrate”) and/or hemicellulose (e.g., xylan, arabinoxylan), as well as lignocellulosic biomass. Biomass can be derived from plants or microorganisms and includes, but is not limited to, agricultural, industrial, and forestry residues, industrial and municipal wastes, and terrestrial and aquatic crops grown for energy purposes. Examples of biomass substrates include, but are not limited to, wood, wood pulp, paper pulp, corn fiber, corn grain, corn cobs, crop residues such as corn husks, corn stover, grasses, wheat, wheat straw, barley, barley straw, hay, rice, rice straw, rice hulls, switchgrass, waste paper, paper and pulp processing waste, woody or herbaceous plants, fruit or vegetable pulp, distillers grain, cotton, hemp, flax, sisal, sugar cane bagasse, sorghum, soy, components obtained from milling of grains, trees, branches, roots, leaves, wood chips, sawdust, shrubs and bushes, vegetables, fruits, and flowers and any suitable mixtures thereof. In some embodiments, the biomass comprises, but is not limited to, cultivated crops (e.g., grasses, including C4 grasses, such as switch grass, cord grass, rye grass, miscanthus, reed canary grass, or any combination thereof), sugar processing residues, for example, but not limited to, bagasse (e.g., sugar cane bagasse, beet pulp [e.g., sugar beet], or a combination thereof), agricultural residues (e.g., soybean stover, corn stover, corn fiber, rice straw, sugar cane straw, rice, rice hulls, barley straw, corn cobs, wheat straw, canola straw, oat straw, oat hulls, corn fiber, hemp, flax, sisal, cotton, or any combination thereof), fruit pulp, vegetable pulp, distillers' grains, forestry biomass (e.g., wood, wood pulp, paper pulp, recycled wood pulp fiber, sawdust, hardwood, such as aspen wood, softwood, or a combination thereof).

Furthermore, in some embodiments, the biomass comprises cellulosic waste material and/or forestry waste materials, including but not limited to, paper and pulp processing waste, municipal paper waste, newsprint, cardboard and the like. Biomass may comprise one species of fiber or a mixture of fibers that originate from different biomasses. In some embodiments, the biomass comprises transgenic plants that express ligninase and/or cellulase enzymes (e.g., U.S. Publication No. 2008/0104724 A1).

As used herein, “lignocellulose” (or “lignocellulosic biomass” or “lignocellulosic substrate”) refers to a matrix of cellulose, hemicellulose and lignin. Economic production of biofuels from lignocellulosic biomass typically involves conversion of the cellulose and hemicellulose components to fermentable sugars, typically monosaccharides such as glucose (from the cellulose) and xylose and arabinose (from the hemicelluloses). Nearly complete conversion can be achieved by a chemical pretreatment of the lignocellulose followed by enzymatic hydrolysis with cellulase enzymes. The chemical pretreatment step renders the cellulose more susceptible to enzymatic hydrolysis and, in some cases, also hydrolyzes the hemicellulose component. Numerous chemical pretreatment processes are known in the art, and include, but are not limited to, mild acid pretreatment at high temperatures and dilute acid, ammonium pretreatment or organic solvent extraction.

Lignin is a more complex and heterogeneous biopolymer than either cellulose or hemicellulose and comprises a variety of phenolic subunits. Enzymatic lignin depolymerization can be accomplished by lignin peroxidases, manganese peroxidases, laccases and cellobiose dehydrogenases (CDH), often working in synergy.

In some embodiments, the biomass is optionally pretreated to increase its susceptibility to enzymatic hydrolysis or degradation to produce a pretreated lignocellulosic substrate. A “pretreated lignocellulosic substrate”, or “pretreated lignocellulose”, is a material of plant origin that, prior to pretreatment, contains 20-90% cellulose (dry wt), more preferably about 30-90% cellulose, even more preferably 40-90% cellulose, for example 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 55, 60, 65, 70, 75, 80, 85, 90% or any % cellulose (dry wt) therebetween, and at least 10% lignin (dry wt), more typically at least 12% (dry wt) and that has been subjected to physical, chemical or biological processes to make the fiber more accessible and/or receptive to the actions of enzymes.

One method of performing acid pretreatment is steam explosion using the process conditions set out in U.S. Pat. No. 4,461,648. Another method of pretreating a biomass slurry involves continuous pretreatment, meaning that the lignocellulosic substrate is pumped though a reactor continuously. Continuous acid pretreatment is familiar to those skilled in the art; see, for example, U.S. Pat. No. 5,536,325; WO 2006/128304; and U.S. Pat. No. 4,237,226. Additional techniques known in the art may be used as required such as the process disclosed in U.S. Pat. No. 4,556,430.

The pretreatment may also be conducted with alkali. In contrast to acid pretreatment, pretreatment with alkali does not typically hydrolyze the hemicellulose component of the lignocellulosic substrate, but rather the alkali reacts with acidic groups present on the hemicellulose to open up the surface of the substrate. The addition of alkali may also alter the crystal structure of the cellulose so that it is more amenable to hydrolysis. Examples of alkali that may be used in the pretreatment include ammonia, ammonium hydroxide, potassium hydroxide, and sodium hydroxide. An example of a suitable alkali pretreatment is Ammonia Freeze Explosion, Ammonia Fiber Explosion or Ammonia Fiber Expansion (“AFEX” process) as described in U.S. Pat. Nos. 5,171,592; 5,037,663; 4,600,590; 6,106,888; 4,356,196; 5,939,544; 6,176,176; 5,037,663 and 5,171,592. The pretreatment is preferably not conducted with alkali that is insoluble in water, such as lime and magnesium hydroxide.

Yet a further non-limiting example of a pretreatment process for use in the present invention includes chemical treatment of the lignocellulosic substrate with organic solvents. Organic liquids in pretreatment systems are described by Converse et al. (U.S. Pat. No. 4,556,430), and such methods have the advantage that the low boiling point liquids easily can be recovered and reused. Other pretreatments, such as the Organosolv™ process, also use organic liquids (see U.S. Pat. No. 7,465,791). Subjecting the lignocellulosic substrate to pressurized water may also be a suitable pretreatment method (see Weil et al. (1997) Appl. Biochem. Biotechnol. 68(1-2): 21-40).

The pretreated lignocellulosic substrate may be processed after pretreatment by any of several steps, such as dilution with water, washing with water, buffering, filtration, or centrifugation, or a combination of these processes, prior to enzymatic hydrolysis, as is familiar to those skilled in the art. The pH of the pretreated lignocellulosic substrate slurry may be adjusted to a value that is amenable to the cellulase enzymes, which is typically between about 4 and about 8.

Biomass-Degrading Enzymes

The following definitions refer to classification of cellulases, hemicellulases and related proteins as defined by the by the Joint Commission on Biochemical Nomenclature of the International Union of Biochemistry and Molecular Biology (Published in Enzyme Nomenclature 1992, Academic Press, San Diego, Calif., ISBN 0-12-227164-5; with supplements in Eur. J. Biochem. 1994, 223, 1-5; Eur. J. Biochem. 1995, 232, 1-6; Eur. J. Biochem. 1996, 237, 1-5; Eur. J. Biochem. 1997, 250; 1-6, and Eur. J. Biochem. 1999, 264, 610-650; also see: chem.qmul.ac.uk/iubmb/enzyme/) and to the Glycoside Hydrolase (GH) families as defined by the CAZy system which is accepted as a standard nomenclature for glycohydrolase enzymes (Coutinho, P. M. & Henrissat, B., 1999, “Carbon-active enzymes: an integrated database approach.” In Recent Advances in Carbon Bioengineering, H. J. Gilbert, G. Davies, B. Henrissat and B. Svensson eds., The Royal Society of Chemistry, Cambridge, pp. 3-12; also see: afmb.cnrs-mrs.fr/CAZY/) and is familiar to those skilled in the art.

Biomass-degrading enzymes are enzymes capable of, or that assist in, breaking down the biopolymers that comprise biomass into smaller oligomers or individual subunits. Typically, biomass-degrading enzymes are hydrolases that can break down cellulose, hemicellulose or related polysaccharides into oligo-, di-, or mono-saccharides, and include but are not limited to, cellulases, glucanases, hemicellulases, and the like.

The terms “biomass-degrading enzyme” also encompasses enzymes and proteins that do not participate directly in the breakdown of cellulose or hemicellulose polymers. Examples of such enzymes and proteins include beta-glucosidases and beta-xylosidases, which convert oligo- and di-saccharides to monosaccharides, acetyl xylan esterases and ferulic acid esterases, which hydrolyze ester linkages between lignin and hemicellulose, and non-hydrolytic proteins, including a variety of cellulase-enhancing proteins.

As used herein, the term “cellulase” refers to any enzyme that is capable of degrading cellulose. The term cellulase (or cellulase enzymes) broadly refers to enzymes that catalyze the hydrolysis of the β-1,4-glucosidic bonds joining individual glucose units in the cellulose polymer. The catalytic mechanism involves the synergistic actions of endoglucanases (E.C. 3.2.1.4) and cellobiohydrolases (E.C. 3.2.1.91). Endoglucanases (or “EG”) hydrolyze accessible glucosidic bonds in the middle of the cellulose chain, while cellobiohydrolases release cellobiose from these chain ends processively. Cellobiohydrolases (or “CBH”) are also referred to as exoglucanases. Most cellulases have a similar modular structure, which consists of one or more catalytic domain and one or more carbohydrate-binding modules (CBM) joined by flexible linker peptides. Most cellulases comprise at least one catalytic domain of Glycoside Hydrolase Family 5, 6, 7, 8, 9, 12, 44, 45, 48, 51, 61 and 74.

A “cellulase-enhancing protein” is a protein that enhances the rate or extent of cellulose hydrolysis by cellulase enzymes but does not exhibit significant cellulose-degrading activity on its own. Cellulase-enhancing proteins include, but are not limited to, proteins classified in Glycoside Hydrolase Family 61, as well as swollenins and expansins.

As used herein, the term “hemicellulase” refers to any enzyme that is capable of degrading hemicellulose. The term hemicellulase broadly refers to enzymes that catalyze the hydrolysis of the glycosidic bonds joining individual sugar units in the hemicellulose polymer. Hemicellulases include, but are not limited to, xylanase (E. C. 3.2.1.8), beta-mannanase (E.C. 3.2.1.78), alpha-arabinofuranosidase (E.C. 3.2.1.55), beta-xylosidases (E.C. 3.2.1.37), and beta-mannosidase (E.C. 3.2.1.25). Hemicellulases typically comprise a catalytic domain of Glycoside Hydrolase Family 1, 3, 5, 8, 10, 11, 26, 30, 39, 43, 51, 52, 54, 62, 113 or 116.

The terms “beta-glucosidase,” “cellobiase,” and “BGL” refer to enzyme members of EC 3.2.1.21 that catalyze the hydrolysis of cellobiose to glucose. Beta-glucosidases typically comprise a catalytic domain of Glycoside Hydrolase Family 1, 3, 5, 9, 30, or 116.

The terms “acetyl xylan esterase” (or “AXE”) and “ferulic acid esterase” (or “FAE”) refer to enzyme members of E.C. 3.1.1.72 and E.C. 3.1.1.73, respectively. AXEs typically comprise a catalytic domain of Carbohydrate Esterase Family 1, 2, 3, 4, 5, 6, 7, 12 or 15 or Glycoside Hydrolase Family 5 or 11, while FAEs typically comprise a catalytic domain of Carbohydrate Esterase Family 1 or Glycoside Hydrolase Family 10 or 78.

The practice of the present invention is not limited by the particular choice of the one or more biomass-degrading enzymes produced by the isolated fungal cells or fermentation processes described herein.

Fermentation Process for Producing Biomass-Degrading Enzymes

The fermentation processes of the present invention comprises culturing an isolated fungal cell with increased or decreased copy number or expression of a PtaB-like protein or a PtaB-encoding nucleotide in a submerged liquid fed-batch or continuous culture.

As used herein, the term “culturing” refers to growing a population of microbial cells under suitable conditions in a liquid or solid medium. The culturing may be carried out using conventional fermentation equipment suitable for such purpose (e.g., shake flasks, fermentation tanks, and bioreactors).

A “submerged liquid culture”, as defined herein, is a microbial culture in which the microbial cells are suspended, or significantly suspended, in a liquid medium containing nutrients required for maintaining the viability of the cells. The culture is generally agitated at a sufficient rate to ensure distribution of the cells throughout the medium. The agitation rate is typically also selected to prevent formation of concentration gradients of nutrients.

In a “batch process” or “batch fermentation”, all the necessary culture and media components, with the exception of oxygen for aerobic processes, are placed in a reactor at the start of the operation and the fermentation is allowed to proceed until completion, at which point the product is withdrawn from the reactor.

In a “fed-batch process” or “fed-batch fermentation”, the culture is fed continuously or sequentially with one or more media components without the removal of the culture fluid.

In a “continuous process” or “continuous fermentation”, fresh medium is supplied and culture fluid is removed continuously at volumetrically equal, or substantially equal, rates to maintain the culture at a steady growth rate. In reference to continuous processes, “steady state” refers to a state in which the concentration of reactants does not vary appreciably, and “quasi-steady state” refers to a state in which, subsequent to the initiation of the reaction, the concentration of reactants fluctuates within a range consistent with normal operation of the continuous hydrolysis process. Continuous fermentation process may also be referred to as CSTR (continuous stirred-tank reactor) fermentations. One example of a continuous fermentation process is a chemostat, in which the growth rate of the microorganism is controlled by the supply of one limiting nutrient in the medium.

In the fermentation processes of the present invention, the fungal cell may be first cultured in a batch fermentation typically containing a non-inducing carbon source. Upon completion of the batch fermentation, which is typically identified by the depletion of essentially all of the available carbon source, for example, when the concentration of the carbon source in the culture filtrate is no more than 1 g/L, the fungal cell is cultured in a fed-batch, continuous or combined fed-batch and continuous submerged liquid culture.

Fed-batch and continuous processes are typically carried out in one or more bioreactors. Typical bioreactors used for microbial fermentation processes include, but are not limited to, mechanically agitated vessels or those with other means of agitation (such as air injection). Bioreactors may be temperature and pH-controlled. Typically, there are means provided to clean the reactor, sometimes in place. Means may also be provided to sanitize or sterilize the bioreactor prior to introduction of the target organism so as to minimize or prevent competition for carbon sources from other organisms. Bioreactors may be constructed from many materials, but most often are of glass or stainless steel. Provisions are generally made for sampling (in a manner that prevents or minimizes the introduction of undesirable competing organisms). Means to obtain other measurements are often provided (e.g., ports and probes to measure dissolved oxygen concentration or concentration of other solutes such as ammonium ions). The practice of the invention is not limited by the choice of bioreactor(s).

In the fermentation processes of the present invention, the fed-batch, continuous or combined fed-batch and continuous submerged liquid culture is provided with a feed solution containing a carbon source. In some embodiments, the carbon source consists of one or more cellulase-inducing carbohydrate, one or more hemicellulose-derived carbohydrate, one or more non-inducing carbohydrate, a mixture of cellulase-inducing and hemicellulose-derived carbohydrate, a mixture of cellulase-inducing and non-inducing carbohydrate, a mixture of hemicellulose-derived and non-inducing carbohydrate, or a mixture of cellulase-inducing, hemicellulose-derived, and non-inducing carbohydrate.

As used herein, the term “carbon source” refers to a carbon-containing substance that provides the major part of the carbon required for growth of, and production of biomass-degrading enzymes by, a parental or isolated fungal cell. For the purposes herein, a carbon source may be one or more carbohydrate, a non-carbohydrate substance such as a sugar alcohol, organic acid, or alcohol, or combinations thereof. However, for the purposes herein, organic nitrogen sources that may be provided to the parental or isolated fungal cell are not considered carbon sources.

As used herein, the term “cellulose-inducing carbohydrate” or “CIC” refers to one or more poly-, oligo- or di-saccharide that leads to the induction of cellulase production by an isolated or a parental fungal cell. By induction, it is meant the switching on of the expression of one or more cellulase genes, whether endogenous or recombinant, in response to the CIC. Non-limiting examples of cellulase-inducing carbohydrates include cellulose, lactose, cellobiose, sophorose, gentiobiose, and a combination thereof. Cellulase-inducing carbohydrate (CIC) may be produced by enzymatic conversion of cellulose with one or more cellulase enzymes to beta-linked glucose dimers. Alternatively, a high concentration glucose syrup can be condensed chemically or enzymatically to form mixtures of glucose dimers. For example, the condensation reaction to convert glucose to CIC may be catalyzed by dilute acid and performed at temperatures above 120-150° C., or by beta-glucosidase or cellulase enzymes at more moderate temperatures of about 40-70° C. (U.S. Publication No. 2004/0121446A1).

As used herein, the term “hemicellulose-derived carbohydrate” or “HDC” refers to one or more poly-, oligo-, di- or mono-saccharide that may be released by the chemical or enzymatic depolymerization of hemicellulose and which can be utilized by an isolated or a parental fungal cell for growth, production of biomass degrading enzymes or both. Non-limiting examples of HDC include xylan, arabinoxylan, xylo-oligosaccharides, arabinoxylo-oligosaccharides, D-xylose, xylobiose, L-arabinose, D-mannose and D-galactose. Preferably, the HDC contains D-xylose and/or L-arabinose.

As used herein, the term “non-inducing carbohydrate” or “NIC” refers to those carbohydrates and other non-carbohydrate carbon sources (e.g., glycerol, sugar alcohols and organic acids), that can be readily metabolized by, but that are known either to have no effect on or to repress the production of biomass degrading enzymes from an isolated or a parental fungal cell. Typically, NIC, when provided alone or in combination with CIC or HDC, results in the production of negligible or very low amounts of biomass degrading enzymes. For the purposes herein, NIC includes, but is not limited to, glucose, dextrose, sucrose, fructose, glycerol, and combinations thereof, whether in pure form or in semi-purified form, such as molasses.

In the fermentation process of the present invention, the feed solution may contain one or more additional components, such as nitrogen sources, vitamins, minerals and salts required for growth of the fungal cell as in known to one of skill in the art. Nitrogen sources may be inorganic and/or organic in nature and include, but are not limited to, one or more amino acids, peptides and proteins, in pure or raw form (e.g., corn steep liquor), any number of protein hydrolysates (peptone, tryptone, casamino acids), yeast extract, ammonia, ammonium hydroxide, ammonium salts, urea, nitrate and combinations thereof. The practice of the fermentation process of the present invention is not limited by the additional components of the feed solution.

The feed solution is provided to the fermentation process at a rate, the feed rate or “carbon addition rate” or “CAR” (measured as g carbon per liter per hour). In the fermentation process of the present invention, the feed solution may be provided to a fed-batch culture at a carbon addition rate of from about 0.2 to about 4 g carbon/L culture/h or any rate therebetween, for example 0.2, 0.3, 0.4, 0.6, 0.8, 1.0, 1.2, 1.4, 1.6, 1.8, 2.0, 2.2, 2.5, 3.0, 3.5, and 4.0 g carbon/L culture/h or any rate therebetween. Alternatively, the feed solution may be provided to a continuous culture at a dilution rate of from about 0.001 to 0.11 h⁻¹, or any dilution rate therebetween, for example at about 0.001, 0.005, 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.11 h⁻¹, or any dilution rate therebetween.

The fermentation processes of the present invention may be carried at a temperature from about 20° C. to about 55° C., or any temperature therebetween, for example from about 30° C. to about 45° C., or any temperature therebetween, or from 20, 22, 25, 28, 30, 32, 35, 38, 40, 42, 45, 48, 50° C., 55° C. or any temperature therebetween.

The fermentation processes of the present invention may be carried out at a pH from about 2.5 to 8.5, or any pH therebetween, for example from about pH 3.5 to pH 7.0, or any pH therebetween, for example from about pH 2.5, 3.0, 3.2, 3.5, 3.8, 4.0, 4.2, 4.5, 4.8, 5.0, 5.2, 5.4, 5.5, 5.7, 5.8, 6.0, 6.2, 6.5, 6.8, 7.0, 7.2, 7.5, 7.8, 8.0, 8.5 or any pH therebetween. The pH may be controlled by the addition of a base, such as ammonium or sodium hydroxide, or by the addition of an acid, such as phosphoric acid.

The fermentation processes of the present invention may be carried out over a period of about 1-90 days, or any period therebetween, for example between 3 and 30 days, or any amount therebetween, between 3 and 8 days, or any amount therebetween, or from 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 40, 50, 60, 70, 80, or 90 days, or any amount therebetween.

The fermentation processes of the present invention may be performed in cultures having a volume of at least 0.5 liter, for example from about 0.5 to about 1,000,000 liters, or any amount therebetween, for example, 5 to about 400,000 liters, or any amount therebetween, 20 to about 200,000 liters, or any amount therebetween, or 2,000 to about 200,000 liters, or any amount therebetween, or from about 0.5, 1, 10, 50, 100, 200, 400, 600, 800, 1000, 2000, 4000, 6000, 8000, 10,000, 15,000, 20,000, 25,000, 30,000, 35,000, 40,000, 45,000, 50,000, 55,000, 60,000, 65,000, 70,000, 75,000, 80,000, 85,000, 90,000, 95,000, 100,000, 150,000, 200,000, 300,000, 400,000, 500,000, 750,000 or 1,000,000 liters in volume, or any amount therebetween.

The fermentation processes of the present invention may be performed aerobically, in the presence of oxygen, or anaerobically, in the absence of oxygen. For example, the process may be performed aerobically such that air or oxygen gas is provided to the submerged liquid culture at a superficial gas velocity of from about 0.001 to about 100 cm/s, or any rate therebetween, for example any rate from about 0.01 to about 20 cm/s, or any rate therebetween. An alternative parameter to measure aeration rate that is known to one of skill in the art is vessel volumes per minute (vvm). In the fermentation process of the present invention, air or oxygen gas is provided to the submerged liquid culture at a rate of from about 0.5 to about 5 vvm, or any rate therebetween. Antifoaming agents (either silicone, or non-silicone based) may be added to control excessive foaming during the process as required and as is known to one of skill in the art.

The fermentation process according to the present invention results in biomass-degrading enzymes being produced from an isolated fungal cell exhibiting increased expression or copy number of a PtaB polynucleotide or increased expression of a PtaB-like proteins. Such fermentation process may result in a population of fungal cells with a 50% reduction in cel-phenotype relative to an equivalent process utilizing a parental fungal cell. Such fermentation process may be characterized by an increase in “sustained productivity” relative to an equivalent fermentation process utilizing a parental fungal cell from which the isolated fungal cell is derived.

As used herein, the term “cel-phenotype” or “cel-” refers to a fungal cell that cannot produce any cellulase protein when provided with a carbon source containing a cellulase-inducing carbohydrate. For example, fungal cells exhibiting a cel-phenotype do not produce halos or clearing zones of digested cellulose around fungal colonies growing on agar media containing a cellulose substrate, as provided in Example 6. Alternatively, fungal cells exhibiting a cel-phenotype do not secrete measurable cellulase protein into culture medium when the fungal cells are grown in liquid culture medium containing a cellulase-inducing carbohydrate.

There are several assays for measuring cellulase activity known to one of skill in the art. Methods to measure cellulase activity are published (e.g., Methods in Enzymology 160, Biomass Part A: Cellulose and Hemicellulose, Wood, W. A. and Kellogg, S. T., eds, Academic Press Inc. 1988; Ghose, T. K. (1987) Pure & Appl. Chem. 59(2):257-268) and include, for example, release of glucose or soluble oligo-saccharides from a cellulose substrate, release of a chromophore or fluorophore from a cellulose derivative, e.g., azo-CMC, or from a small, soluble substrate such as methylumbelliferyl-beta-D-cellobioside, para-nitrophenyl-beta-D-cellobioside, para-nitrophenyl-beta-D-lactoside and the like. For example, hydrolysis of cellulose can be monitored by measuring the enzyme-dependent release of reducing sugars, which are quantified in subsequent chemical or chemienzymatic assays known to one of skill in the art, including reaction with dinitrosalisylic acid (DNS). In addition, cellulose or colorimetric substrates (cellulose derivatives or soluble substrates) may be incorporated into agar-medium on which a host microbe expressing and secreting one or more cellulase enzymes is grown. In such an agar-plate assay, activity of the cellulase is detected as a coloured or colourless halo around the individual microbial colony expressing and secreting an active cellulase.

As used herein, the term “specific productivity”, alternatively expressed as “q_(p)”, refers to the rate at which secreted protein is produced from a given mass of fungal cells. Typically, the specific productivity of a fermentation process is expressed as mg protein per g of fungal cells per hour (mg protein/g cells/h) and is calculated by measuring the concentration, in mg/L, of protein in culture filtrates (culture media from which the fungal cells have been removed) and dividing by the concentration of fungal cells (in g dry weight per L) in the culture medium and dividing by the total time, in h, since the feed solution was initially provided to the culture. The fermentation processes of the present invention may also be characterized by “maximum productivity” (or “maximum q_(p)”), which is the highest value q_(p) calculated during the course of the fermentation process, or by “average productivity” (or “average q_(p)”), which is the average of all of the values of q_(p) calculated during the course of the fermentation process

Methods to measure concentration of secreted protein in culture filtrates include the methods of Bradford (Bradford, M. M. et al. (1976) Anal. Biochem. 72: 248-254), Lowry (Lowry O H, et al. (1951) J. Biol. Chem. 193: 265-175), and Smith (Smith, P. K., et al. (1985). Anal. Biochem. 150: 76-85). Increased production of individual cellulase enzymes can be measured, for example, with immunochemical methods such as ELISA (Van Weemen, B. K. et al. (1971) FEBS Letters 15: 232-236) with antibodies specific to the individual enzyme. Methods to measure concentration of fungal cells, in g dry weight per L of culture medium, are provided in Example 5.

As a result of the decreased population of fungal cells exhibiting a cel-phenotype, fermentation processes conducted at a CAR less than 1 g carbon per liter per hour, for example at a CAR of 0.4 g/l/h), and utilizing an isolated fungal cell comprising increased expression or copy number of a PtaB polynucleotide or increased expression of a PtaB-like protein may be characterized by an increase in sustained productivity. By “sustained productivity” or “sustained q_(p)”, it is meant the number of hours during which a fermentation process exhibits at least 70% of its maximum productivity or maximum q_(p). As shown in FIGS. 7 and 8, fermentation processes with isolated fungal cells comprising increased expression or copy number of a PtaB polynucleotide or increased expression of a PtaB-like proteins, have a longer sustained q_(p) relative to equivalent fermentation processes utilizing the parental fungal cell.

According to one aspect of the present invention, there is provided a fermentation process in which the one or more biomass-degrading enzyme is produced from an isolated fungal cell exhibiting increased expression or copy number of a PtaB polynucleotide, or increased expression of a PtaB-like proteins, wherein the process results in a population of fungal cells with at least a 50% reduction in cel-phenotype relative to an equivalent process utilizing a parental fungal cell. For example, such fermentation process may result in a population of fungal cells with at least a 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% reduction, or any amount therebetween, in cel-phenotype. Typically, this reduction in cel-phenotype is observed in the fungal cell population after at least about 96 hours after the initiation of the fed-batch or continuous culturing step. For example, the reduction in cel-phenotype may be observed in the fungal cell population after at least about 96 h, 108 h, 120 h, 132 h, 144 h, 156 h, 168 h, 180 h, 192 h, 204 h, or any time therebetween or later, after the initiation of the fed-batch or continuous culturing step. Such fermentation process may also be characterized by a specific productivity that is equal to or higher than that of an equivalent fermentation process utilizing a parental fungal cell from which the isolated fungal cell is derived.

A fermentation process according to the present invention in which the one or more biomass-degrading enzyme is produced from an isolated fungal cell exhibiting decreased expression or copy number of a PtaB polynucleotide, or decreased expression of a PtaB-like protein, exhibits at least a 50% increase in maximum specific productivity (q_(p)) relative to that exhibited by an equivalent process utilizing a parental fungal cell from which the isolated fungal cell is derived. For example, such fermentation process may exhibit at least a 50%, 60%, 70%, 80%, 90%, 100%, 150%, 200%, 300%, 400%, 500% or higher increase in maximum specific productivity (q_(p)) relative to that exhibited by an equivalent process utilizing a parental fungal cell from which the isolated fungal cell is derived.

As used herein, the terms “equivalent fermentation process” or “equivalent process”, refer to a fermentation process in which a parental fungal cell is cultured under identical or nearly identical conditions of medium composition, time, cell density, temperature, and pH, as those used to culture an isolated fungal cell derived from that parental fungal cell.

Use of Biomass-Degrading Enzymes

The one or more biomass-degrading enzymes produced by the isolated fungal cell and/or fermentation processes of the present invention may be used in process to convert biomass to soluble sugars.

As contemplated herein, a biomass substrate may be treated with one or more biomass-degrading enzymes produced by the isolated fungal cell and/or fermentation processes of the present invention to produce soluble sugars. Examples of soluble sugars include, but are not limited to, glucose, cellobiose, cellodextrins, xylose, arabinose, galactose, mannose or mixtures thereof. The soluble sugars may be predominantly cellobiose and glucose.

Treatment of the biomass substrate with the one or more biomass-degrading enzymes may be carried out at a pH and temperature that is at or near the optimum for the biomass-degrading enzyme(s). For example, the treatment may be carried out at about 30° C. to about 75° C., or any temperature therebetween, for example a temperature of 30, 35, 40, 45, 50, 55, 60, 65, 70, 75° C., or any temperature therebetween, and a pH of about 3.5 to about 8.0, or any pH therebetween, for example a pH of 3.5, 4.0, 4.5, 5.0, 5.5, 6.0, 6.5, 7.0, 7.5, 8.0 or any pH therebetween.

The initial concentration of biomass substrate at the start of the treatment process is preferably about 0.01% (w/w) to about 20% (w/w), or any amount therebetween, for example 0.01, 0.05, 0.1, 0.5, 1, 2, 4, 6, 8, 10, 12, 14, 15, 18, 20% or any amount therebetween. The combined dosage of all biomass-degrading enzymes may be about 0.001 to about 100 mg protein per gram substrate, or any amount therebetween, for example 0.001, 0.01, 0.1, 1, 5, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100 mg protein per gram substrate or any amount therebetween.

The treatment process may be carried out for a time period of about 0.5 hours to about 200 hours, or any time therebetween, for example, the treatment process may be carried out for a period of 2 hours to 100 hours, or any time therebetween, or it may be carried out for 0.5, 1, 2, 5, 7, 10, 12, 14, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 120, 140, 160, 180, 200 hours or any time therebetween.

The treatment process may be conducted as a batch, continuous, or a combined batch and continuous reaction, which may be agitated, unmixed, or a combination thereof. The treatment process is typically carried out in a reactor. The one or more biomass-degrading enzymes may be added to the biomass substrate prior to, during, or after the addition of the substrate to the hydrolysis reactor.

It should be appreciated that the reaction conditions are not meant to limit the invention in any manner and may be adjusted as desired by those of skill in the art.

EXAMPLES Example 1: Host Trichoderma Strains for the Deletion and Overexpression of ptaB Gene

The host Trichoderma reesei strains used for the deletion of ptaB gene is M2C38aux derived from strain Rut-C30. Strain Rut-C30 (ATCC Deposit No. 56765) was isolated as a high cellulase producing derivative of progenitor strain QM6a (Montenecourt and Eveleigh, 1979, supra). Cellulase hyper-producing strains were generated from Rut-C30 by random mutation and/or selection. Strain M2C38 was isolated based on its ability to produce larger clearing zones than Rut-C30 on minimal media agar containing 1% acid swollen cellulose and 4 g/L 2-deoxyglucose. The ura3 auxotroph of strain M2C38 (strain M2C38aux), deficient in uracil production, was isolated based on the ability to grow on minimal media agar supplemented with 5 mM uridine and 0.15% (w/v) of 5-fluoro-orotic acid.

The host Trichoderma reesei strain used for the overexpression of ptaB gene is BTR213, which is derived from strain M2C38. BTR213 was isolated during random mutagenesis and selection for ability to produce larger clearing zones on minimal media agar containing 1% acid swollen cellulose and 4 g/L 2-deoxyglucose followed by selection on lactose media containing 0.2 μg/mL carbendazim. The ura3 auxotroph of strain BTR213 (strain BTR213aux), deficient in uracil production, was isolated based on the ability to grow on minimal media agar supplemented with 5 mM uridine and 0.15% (w/v) of 5-fluoro-orotic acid. BTR213 strain contains C432T mutation the PtaB-like protein of SEQ ID NO: 1. This mutation results in substitution of glutamine codon to stop codon and truncation of protein to 118 amino acids in length instead of 721 amino acids.

Example 2: Construction of Trichoderma reesei ptaB Deletion Cassette Example 2.1: Trichoderma reesei Genomic DNA Isolation and Amplification of ptaB (EGR46093.1) Flanking Sequences

For genomic DNA isolation, T. reesei spores collected from a Potato Dextrose Agar (PDA) plate were inoculated in 50 mL of Potato Dextrose Broth (PDB) (Difco™) The cultures were shaken at 200 rpm for 2-3 days at 28° C. The mycelia were filtered onto a glass fiber circles (GFA) (Fisher Cat. #09-804-424) and washed with cold, deionized water. The fungal cakes were frozen in liquid nitrogen and crushed into a powder with a pre-chilled mortar and pestle; 0.5 g of powdered mycelia was resuspended in 5 mL of buffer containing 100 mM Tris, 50 mM EDTA, pH 7.5 and 1% sodium dodecyl sulphate (SDS). The lysate was centrifuged (5000×g for 20 min at 4° C.) to pellet cell debris. The supernatant was extracted with 1 volume of TE buffer (10 mM Tris, 1 mM EDTA, pH 8.0) saturated phenol followed by extraction with 1 volume of buffer-saturated phenol:chloroform:isoamyl alcohol (25:24:1). Genomic DNA was precipitated from the solution by adding 0.1 volume of 3 M sodium acetate, pH 5.2 and 2.5 volumes of cold 95% ethanol. After incubating for at least 1 h at −20° C., the DNA was pelleted by centrifugation (5000×g for 20 min at 4° C.), rinsed with 10 mL of 70% ethanol, air-dried and resuspended in 1 mL of TE buffer. The RNA was digested by the addition of Ribonuclease A (Sigma-Aldrich) (final concentration of 0.1 mg/mL) and incubation at 37° C. for 1 hour. Ribonuclease was removed by extracting with 1 volume of buffer-saturated phenol and 1 volume of buffer-saturated phenol:chloroform:isoamyl alcohol (25:24:1). The DNA was precipitated with 0.1 volumes of 3 M sodium acetate, pH 5.2 and 2.5 volumes of cold 95% ethanol, pelleted by centrifugation, rinsed with 70% ethanol, air-dried and resuspended in 0.05 mL of TE buffer. The concentration of DNA was determined by measuring the absorbance of the solution at 260 nm.

A DNA fragment comprising 274 nucleotides of the 3′ end of PtaB coding sequence and 1374 nucleotides of the ptaB terminator and 3′ flanking sequences (SEQ ID NO:) was amplified from T. reesei genomic DNA using iProof® High Fidelity DNA polymerase (Bio-Rad) and following primers: forward—AC985 GAACCTCCCGGGGTCGCCTCACATC (SEQ ID NO: 15) and reverse—AC986 GCTGCAACGAACGTCCTTTGCATC (SEQ ID NO: 16). The PCR was performed according to manufacturer's protocol with an annealing temperature of 60° C. and 75 seconds extension time for 30 cycles. The 1.65 kb amplicon was gel extracted and purified with the Wizard® SV Gel and PCR Clean-up System (Promega). The purified PCR product was used as a template for a second PCR to add overhangs homologous to vector sequences for recombinase-based cloning with the following primers: forward—AC987 TGAAGCCGATGTCACACGCGTGAACCTCCCGGGGTCGCCTCACATC (SEQ ID NO: 17) and reverse—AC988 ACGCAGCTAGCAGCTGGTACCGCTGCAACGAACGTCCTTTGCATC (SEQ ID NO: 18). The PCR was performed according to manufacturer's protocol with an annealing temperature of 60° C. and 75 seconds extension time for 30 cycles. The 1.65 kb amplicon was gel extracted and purified with the Wizard® SV Gel and PCR Clean-up System (Promega).

A 1.97 kb DNA fragment containing the ptaB promoter and 5′ flanking sequences was amplified from T. reesei genomic DNA using iProof® High Fidelity DNA polymerase (Bio-Rad) and the following primers: forward—AC956 CTCTCGATGATGCGTGTAAG (SEQ ID NO: 19) and reverse—AC957 CCATACTCGTAGCCATCATC (SEQ ID NO: 20). The PCR was performed according to manufacturer's protocol with an annealing temperature of 60° C. and 75 seconds extension time for 30 cycles. The 1.97 kb amplicon was gel extracted and purified with the Wizard® SV Gel and PCR Clean-up System (Promega). The purified PCR product was used as a template for a second PCR to add overhangs homologous to vector sequences for recombinase-based cloning with the following primers: forward—AC989 GTACTGAGAGTGCACCATATGCTCTCGATGATGCGTGTAAG (SEQ ID NO: 21) and reverse—AC990 TCGGTTCTTAATTAAGAATTCCCATACTCGTAGCCATCATC (SEQ ID NO: 22). The PCR was performed according to manufacturer's protocol with an annealing temperature of 60° C. and 75 seconds extension time for 30 cycles. The 1.97 kb amplicon was gel extracted and purified with the Wizard® SV Gel and PCR Clean-up System (Promega).

Example 2.2: Construction of the ptaB Deletion Vector

The PCR product containing the ptaB 3′ coding sequence, terminator and 3′ flank was recombined into a vector containing ura3 selection marker cassette, pTrBxl1p-NheI-KpnI-Tr7at-Ura3, digested MluI/KpnI using In-Fusion® Cloning Kit (Clontech) to produce an intermediate vector. The recombination reaction was completed according to the manufacturer's protocol. The PCR product containing the ptaB promoter and 5′ flank was recombined into the intermediate vector digested EcoRI/NdeI to yield the deletion cassette containing ura3 selection marker cassette flanked with 5′ and 3′ ptaB targeting sequences. The full 6.97 kb deletion cassette was then amplified by PCR with primers: forward—AC956 CTCTCGATGATGCGTGTAAG (SEQ ID NO: 19) and reverse—AC986 GCTGCAACGAACGTCCTTTGCATC (SEQ ID NO: 16) and iProof® High Fidelity DNA polymerase (Bio-Rad). The PCR reaction was performed according to the manufacturer's protocol with an annealing temperature of 60° C. and 5 minutes of extension time for 30 cycles. The 6.97 kb PCR product was purified using the Wizard® SV Gel and PCR clean-up System (Promega) and cloned into the pJET1.2™ (Fermentas) resulting in the vector pJET-ptaB-delta-ura3 (FIG. 1).

Example 3: Generation of Isolated Fungal Cells by Deletion of PtaB-Encoding Polynucleotide

The pJET-ptaB-delta-ura3 transformation vector was introduced into T. reesei strain M2C38aux using the PEG-mediated protoplast transformation method. Approximately 5×10⁶ spores of M2C38aux were plated onto sterile cellophane placed on PDA supplemented with 5 mM uridine and incubated for 20 hours at 30° C. Cellophane discs with mycelia were transferred to 10 mL of a protoplast preparation solution containing 7.5 g/L Driselase® Basidiomycetes sp. (Sigma) and 4 g/L beta-glucanase (InterSpex Products Inc.) in 50 mM potassium phosphate buffer, pH 6.5 containing 0.6 M ammonium sulfate (Buffer P). The mycelia were digested for 5 hours at 28° C. with gentle agitation at 60 rpm. Protoplasts were collected by centrifugation at 1000-1500×g for 10 min at room temperature and washed with 5 mL of Buffer P. The pellet was resuspended in 1 mL of STC buffer (1.2 M sorbitol, 10 mM CaCl₂, 10 mM Tris-HCl, pH 7.5), separated from undigested mycelia by filtration through sterile 30 μM Nylon Net filter (Millipore) and collected into a sterile microcentrifuge tube. For transformation, 0.1 mL of protoplast suspension (approximately 5×10⁶ protoplasts) was combined with 10 μg of BglII digested vector DNA, and 25 μL of PEG solution (25% PEG 4000, 50 mM CaCl₂, 10 mM Tris-HCl, pH 7.5). Protoplasts with DNA were incubated on ice for 30 min then 1 mL of PEG solution was added and the mixture incubated for 5 min at room temperature. Transformation mix was diluted with 2 mL of 1.2 M sorbitol in PEG solution.

The transformation mix with BglII linearized pJET-ptaB-delta-ura3 plasmid and protoplasts of strain M2C38aux were added into 50 mL of molten MMSS agar media (see below) cooled to 50° C. and the protoplast suspension was split over two MM agar (see below) plates. Plates were incubated at 30° C. until colony growth was visible. Transformants were transferred to individual plates containing MM agar and allowed to sporulate. Spores were collected and plated at high dilution on MM agar to isolate homokaryon transformants, which were then plated onto PDA (Difco™) and incubated at 30° C. for sporulation and subsequent genetic analysis.

Minimal medium (MM) agar: Component* Amount for 1L of medium KH₂PO₄ 10 g (NH₄)₂SO₄ 6 g Na₃Citrate•2H₂O 3 g FeSO₄•7H₂O 5 mg MnSO₄•H₂O 1.6 mg ZnSO₄•7H₂O 1.4 mg CaCl₂•2H₂O 2 mg Agar 20 g 20% Glucose f.s. 50 mL 1M MgSO₄•7H₂O f.s. 4 mL pH to 5.5 *MMSS agar contains the same components as MM agar plus 1.2M sorbitol, 4 mM MgSO₄, 1 g/L YNB (Yeast Nitrogen Base w/o Amino Acids from DIFCO Cat. No. 291940) and 0.12 g/L amino acids (-Ura DO Supplement from Clontech Cat. No. 8601-1).

Example 4: Genetic Characterization of Isolated Fungal Cells

The deletion of the PtaB-encoding gene in isolated fungal cells was assessed by PCR on extracted genomic DNA samples using specific primers as described below. For genomic DNA extraction protoplasts from mitotically stable transformants were prepared as for PEG-mediated transformation described in Example 3. DNA was then extracted from the protoplasts using the Wizard® Genomic DNA Purification Kit (Promega, Cat. #A1120) as described in manufacture's protocol. One microliter of genomic DNA was used for PCR reactions.

Initially, PCR analysis of the genomic DNA isolated from filamentous fungi transformants was used to identify if the deletion cassette integrated into ptaB locus. The PCR was performed using pair of primers, forward—AH439 GATGATGGCTACGAGTATGG (SEQ ID NO: 23), reverse—AH440 GGGAATCGAGCAAGTAAGAG (SEQ ID NO: 24), and iProof® High Fidelity DNA polymerase (Bio-Rad). The PCR was performed in 30 cycles with an annealing temperature of 62° C. and 110 seconds of extension time. Positive transformants (deletion of the native ptaB gene) were identified by an amplification of a 3.7 Kb product (FIG. 2). Negative transformants (contain native ptaB gene) were identified by amplification of a 2.6 Kb product. No 3.7 Kb PCR products were detected for the parent strain M2C38aux (FIG. 2). Five PtaB deletion strains were identified and selected for confirmation of deletion by Southern blotting. Probe for Southern blotting was synthesized and labeled using PCR DIG Probe Synthesis Kit (Roche, Cat #11 636 090 910) and primers, forward—AC956 CTCTCGATGATGCGTGTAAG (SEQ ID NO: 19) and reverse—AC957 CCATACTCGTAGCCATCATC (SEQ ID NO: 20). PCR reaction was performed following manufacture's recommendation with annealing temperature of 58° C. and extension time of 80 seconds. Synthesized 1966 bp PCR product, homologous to by −1993 to by −27 upstream of the ptaB start codon, was purified using Wizard® SV Gel and PCR clean-up System (Promega). For Southern blotting, genomic DNA isolated from putative PtaB deletion strains and their parental strain M2C38 was digested with SalI restriction enzyme and separated by agarose gel electrophoresis. The transformation vector was loaded on the gel as a control. The capillary DNA transfer to positively charged nylon membrane, hybridization of probe to target using DIG Easy Hyb buffer (Roche Cat #11 603 558 001) and detection of probe-target hybrids using NBT/BCIP (Roche Cat. #11 681 451 001) were performed as described in “DIG Application Manual” (Roche). The hybridization temperature was 68° C., two low stringency washes after hybridization were performed using 2×SSC containing 0.1% SDS at room temperature for 5 min and two high stringency washes were performed in 0.5×SSC containing 0.1% SDS at 68° C. for 15 min. The Southern blotting confirmed that all transformants selected by PCR analysis contain deletion of ptaB.

Example 5: Production of Biomass-Degrading Enzymes from Isolated and Parental Fungal Cells

Trichoderma spores from frozen (−80° C.) 15% glycerol stocks of strain M2C38 and a selected ptaB deletion strain, were inoculated onto standard 85 mm Petri plates containing potato dextrose agar (PDA). These plates were incubated at 28° C. for 5 days to achieve a confluent growth of fresh spores. To prepare the inoculum for fermentation testing, spores from a single PDA plate were transferred to a 2 L, baffled Erlenmeyer flask containing 750 mL of liquid Berkley media (pH 5.5) supplemented with 5.1 g/L of corn steep liquor powder and 10 g/L glucose. Flasks were incubated at 28° C. for 3 days using an orbital agitator (Model G-52 New Brunswick Scientific Co.) running at 100 rpm.

Berkley Media, for Flasks Component g/L (NH₄)₂SO₄ 10.4 KH₂PO₄  2.0 MgSO₄•7H₂O  0.31 CaCl₂•2H₂O  0.53 Dry Corn Steep Liquor  5.1 Glucose 10 Trace elements*  1 mL/L *Trace elements solution contains 5 g/L FeSO₄•7H₂O; 1.6 g/L MnSO₄•H₂O; 1.4 g/L ZnSO₄•7H₂O.

The contents of an inoculum flask were transferred to a 14 L pilot scale fermentation vessel (Model MF114 New Brunswick Scientific Co.) set up with 10 L of Initial Pilot Media (pH 5.5). The vessel was run in batch mode until glucose in the media was depleted. At this point, the feed solution containing cellulase inducing carbohydrate as the carbon source was added at a carbon addition rate (CAR) of either 0.4 g of carbon per liter per hour or 1.0 g per liter of culture per hour. Peristaltic pumps were used to deliver the carbon source at a feed at a rate of 0.4 grams of carbon per liter culture per hour. Operational parameters during both the batch and fed-batch portions of the run were: mixing by impeller agitation at 500 rpm, air sparging at 8 standard liters per minute, and a temperature of 28° C. Culture pH was maintained at 4.0-4.5 during batch growth and pH 3.5 during cellulase production using an automated controller connected to an online pH probe and a pump enabling the addition of a 10% ammonium hydroxide solution. Periodically, 100 mL samples of broth were drawn for biomass and protein analysis. The total fermentation time typically is 168 hours; however for fermentations conducted at a CAR of 0.4 g of carbon per liter per hour, the total fermentation time was extended to 216 hours.

Initial Media for Fed-Batch Fermentations Component g/L (NH₄)₂SO₄  2.20 KH₂PO₄  1.39 MgSO₄•7H₂O  0.70 CaCl₂•2H₂O  0.185 Dry Corn Steep Liquor  6.00 Glucose 13.00 Trace elements*  0.38 mL/L *Trace elements solution contains 5 g/L FeSO₄•7H₂O; 1.6 g/L MnSO₄•H₂O; 1.4 g/L ZnSO₄•7H₂O.

The biomass content of the culture broth was determined using aliquots of 5-10 mL that had been weighed, vacuum filtered through glass microfiber filters, and oven dried at 100° C. for 4 to 24 hours. The concentration of biomass was determined according to the equation below.

${{Biomass}\;\left( {g\text{/}L} \right)} = {\frac{{{dry}\mspace{14mu}{filter}\mspace{14mu}{paper}\mspace{14mu}{and}\mspace{14mu}{cake}\;(g)} - {{filter}\mspace{14mu}{mass}\;(g)}}{{wet}\mspace{14mu}{sample}\mspace{14mu}{mass}\;(g)} \times {broth}\mspace{14mu}{density}\;\left( {g\text{/}{mL}} \right) \times 1000\;\left( {{mL}\text{/}L} \right)}$

The protein concentration of culture filtrate was determined using the Bradford assay. Colour intensity changes in the Coomassie Brilliant Blue G-250 dye, that forms the basis of this assay, were quantified spectrophotometrically using absorbance measurements at 595 nm. The standard assay control used was a cellulase mixture of known composition and concentration. The specific productivity, q_(p), was expressed as mg protein produced per gram of biomass per hour of fermentation.

The fermentation profiles of a Trichoderma reesei PtaB deletion strain and its parental strain M2C38 grown at CAR of 1.0 and ˜0.4 g carbon/L/h are shown in FIGS. 3 and 4, respectively. At the 168 hr fermentation time, the PtaB deletion strain produced 82.9% and 16.8% more of total protein, respectively, compared to that of its parental strain M2C38. In addition, the fermentation of the parental strain M2C38 conducted at a CAR of 0.4 g of carbon per liter per hour exhibited a higher sustainability productivity during extended fermentation run.

Example 6: Evaluation cel-Phenotype in Fungal Cell Populations

Since specific productivity of P1587AD transformant at the end of fermentation significantly decreased, the ability of cells collected at 168 h from fermentation start to produce cellulases was tested by plating on acid swollen cellulose plates. Preparation of phosphoric acid swollen cellulose (ASC) was conducted as follows. 400 g of SIGMACel T50 was wetted with 600 mL of acetone and mixed thoroughly with a paddle mixer in a 20 L bucket. The bucket content was then cooled in an ice water bath. A total of 4 L of commercial grade phosphoric acid (85%) was slowly added to the wetted cellulose and the suspension constantly stirred. Precooled deionized water was added to the acid/cellulose gelatinous mixture resulting in precipitation of a white clumpy material. A solution of 5-7% bicarbonate was added to begin neutralizing the slurry. The solution was slowly added to the slurry with constant mixing. Once the slurry pH is 5-7, it can be filtered through GF/A filter paper by vacuum filtration. The moist white cellulose preparation was washed with greater than 4 L of deionized water to ensure salts, and soluble sugars were removed from the resulting amorphous cellulose. Typical solids content of the cellulose after acid treatment is 7-9%. Further ASC was homogenized using the Powergen 1000 homogenizer (Fisher Scientific), diluted with an equal volume of water and pH adjusted to 4.5-4.6 before blending for 1 minute in a standard kitchen blender followed by sterilizing in the autoclave at standard temperatures and pressures. At this point the concentration of ASC is 25 g/L.

Biomass samples were collected at 168 hours from fermentation start, plated on PDA plates and incubated at 30° C. for 5 days to allow sporulation. The spores were washed from PDA plates with sterile water and about 50-100 spores were spread on ASC-minimal media containing 10 g/L of ASC and 7 g/L of Oxga11. ASC plates were incubated at 30° C. for 6 days, and transferred to 50° C. for 20 h. Cellulase secretion by individual colonies was assessed by formation of clearing zone around colonies. The non-producing colonies were counted; the proportion in total cell population was calculated and is presented in FIG. 5. The deletion of ptaB resulted in high population of cellulase non-producing phenotypes developed at the end of fermentation.

Component Amount per liter of media 5X Minimal Media Salts* 40 mL Proteose Peptone#3 (Difco ™) 0.2 g Bovine Oxgall (Difco ™) 1.8 g Agar 4 g Deionzed water 80 mL Phosphoric Acid Swollen 80 mL Cellulose (25 g/L) 1M MgSO₄•7H₂O 4 mL *ASC-Minimal Media Composition

Component Amount per liter of media KH₂PO₄ 50 g (NH₄)₂SO₄ 30 g Na₃-Citrate•2H₂O 15 g FeSO₄•7H₂0 25 mg MnSO₄•H₂O 8 mg ZnSO₄•7H₂O 7 mg CaCl₂•2H₂O 10 mg *5X Minimal Media Salts Composition

Example 7: Overexpression of PtaB in Trichoderma reesei Example 7.1: Generation of PtaB-Like Protein Overexpressing Transformants

PtaB encoding polynucleotides were PCR amplified from genomic DNA isolated from T. reesei strain QM6a. Pair of primers, forward AC671 5′-TTGCTAGCATGGGACATCCTGGAGTTG-3′ (SEQ ID NO: 25) and reverse—AC683 5′-TTGGTACCTCAGGCCGGGTTGCCCTTCATTC-3′(SEQ ID NO: 26), was used to introduced NheI and KpnI sites required for cloning into transformation vector pTrBxl1p-NheI-KpnI-Tr7at-Ura3. This vector contains T. reesei ura3 gene as selection marker for Trichoderma transformation and cassette for expression of gene of interest. The amplified fragment was cloned into pJET vector (Fermentas). The coding sequence then was digested out of pJET with NheI/KpnI restriction enzymes and ligated into the same sites of pTrBxl1p-NheI-KpnI-Tr7at-Ura3, between beta-xylosidase (bxl) promoter and cellobiohydrolase I (cel7a) terminator. The generated T. reesei transformation vector pTrBxl1p-ptaB-Tr7at-Ura3 (FIG. 6) was used for transformation of BTR213aux strain.

The transformation was performed by biolistic gold particle bombardment using PDS-1000/He system with Hepta adapter (Bio-Rad; E.I. DuPont de Nemours and Company). Gold particles (median diameter of 0.6 um, Bio-Rad Cat. No. 1652262) were used as microcarriers. Prior transformation T. reesei was grown on potato dextrose agar (PDA) (Difco™) plates for 4-5 days at 30° C. until sporulated. Spores were suspended in sterile water. About 3.5×10⁸ of spores was plated on 100 mm diameter plates containing minimal media (MM). The following parameters were used for the transformation: a rupture pressure of 1350 psi, a helium pressure of 28 mm Hg, target distance 3 cm. After particle delivery spores from each transformation plate were washed off with 2.5 mL of sterile 0.9% NaCl, spread on 3-4 150 mm plates containing MM (described in Example 3) and incubated at 30° C. for 5-10 days. All transformants were transferred to PDA media and incubated at 30° C. until sporulation.

Example 7.2: Screening of PtaB-Like Protein Overexpressing Transformants on ASC Plates

Phosphoric acid swollen cellulose (ASC) was prepared and assessment of cellulase production by 29 Trichoderma transformants overexpressing the PtaB-like protein was performed as described in Example 6. The largest clearing zone-producing transformant was selected for further characterization in 14 L pilot fermentations.

Example 7.3: Analysis of PtaB Overexpressing Strains in 14 L Pilot Fermentations

All pilot fermentations of parental strain BTR213 and PtaB overexpression strain were performed as described in example 5. For induction of the beta-xylosidase promoter directing expression of the PtaB-like protein, a mixture of 25 wt % xylose and 75 wt % CIC was used as the carbon source. Fermentation profiles of both strains grown in high (1.0) and low (0.4) CAR conditions are shown in FIGS. 7 and 8. In high CAR conditions (CAR 1.0 g carbon per liter per h) PtaB overexpression strain produced about 35% less of total protein and about 75% more of biomass compared to parental strain. Both strain show a similar drop in specific productivity at the end of fermentation. In contrast, at a CAR of 0.4 g carbon per liter per h, the fermentation using the PtaB overexpression strain sustained its specific productivity until the end of fermentation while maintaining the same level of protein productivity as parental strain (FIG. 8).

The accumulation of non-cellulase producing phenotype at the end of fermentations was evaluated as described in example 6. The accumulation of non-cellulase producing phenotype in BTR213 strain fermentation reached almost 40%, while all of the cells in fermentation with the PtaB overexpressing strain were still producing cellulases at the end of fermentation (FIG. 9). 

The invention claimed is:
 1. An isolated fungal cell capable of producing one or more biomass-degrading enzyme, comprising a decrease in copy number or expression, relative to a parental fungal cell from which the isolated fungal cell is derived, of a polynucleotide that encodes a polypeptide exhibiting from about 50% to 100% identity to SEQ ID NO: 1 or from about 60% to about 100% identity to the amino acid sequence of SEQ ID NO: 3, SEQ NO: 4, SEQ NO: 5, SEQ ID NO: 7, SEQ NO: 9, SEQ NO: 11, or SEQ ID NO: 14, wherein (a) the fungal cell is a species of Trichoderma, Hypocrea, Aspergillus, Fusarium, Penicillum, Chaetomium, Acremonium, Glomerella, Myceliophthora, Sporotrichum, Thielavia, Chrysosporium, Corynascus, Ctenomyces, Vertucillium, Cordyceps, Nectria, or Magnaporthe and (b) the fungal cell, when cultured in a fed-batch or continuous culture fermentation provided with a feed solution comprising a carbon source, exhibits at least about a 50% increase in maximal specific productivity (q_(p)) relative to a parental fungal cell from which the isolated fungal cell is derived cultured under the same conditions.
 2. The fungal cell of claim 1, wherein the polypeptide exhibits from about 60% to about 100% identity to the amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 7, or SEQ ID NO:
 9. 3. The fungal cell of claim 2, wherein the one or more biomass-degrading enzyme is selected from the group consisting of a cellulase, a cellobiohydrolase, an endoglucanase, a beta-glucosidase, a cellulase-enhancing, protein, a xylanase, a beta xylosidase, an alpha-arabinofuranosidase, a beta-mannanase, an alpha-glucuronidase, an acetyl xylan esterase, a ferulic acid esterase, a lignin-degrading enzyme, and a combination thereof.
 4. The fungal cell of claim 3, wherein at least one of the one or more biomass-degrading enzymes is endogenous to the fungal cell.
 5. The fungal cell of claim 3, wherein at least one of the one or more biomass-degrading enzymes is heterologous to the fungal cell.
 6. The fungal cell of claim 1, wherein the fungal cell is T. reesei, jecorina, A. niger, A. fumigatus, A. orzyae, A. nidulans, F. oxysporum, C. thermophilum, A. thermophilum, G. graminicola, thermophila, thermophile, T. terrestris, T. heterothallica, C. thermophile, V. dahlia, C. militaris, N. heamatococca, or M. orzyae.
 7. A fermentation process for the production of one or more biomass-degrading enzyme, said process comprising: (a) providing the isolated fungal cell of claim 1; (b) culturing the isolated fungal cell in a submerged liquid fed-batch or continuous culture; and (c) providing the fed-batch or continuous culture with a feed solution comprising a carbon source, wherein the process is characterized by having at least about a 50% increase in maximal specific productivity (q_(p)) relative to an equivalent process utilizing a parental fungal cell from which the isolated fungal cell is derived.
 8. The fermentation process of claim 7, wherein the carbon addition rate is at least 0.8 grams of carbon per liter per hour.
 9. The fermentation process of claim 7 or 8, wherein the step of culturing is provided with feed solution comprising a carbon source consisting of: (a) one or more cellulase-inducing carbohydrate; (b) one or more hemicellulose-derived carbohydrate; (c) one or more non-inducing carbohydrate; (d) a mixture of (a) and (b); (e) a mixture of (a) and (c); (f) a mixture of (b) and (c); or (g) a mixture of (a), (b) and (c).
 10. The fermentation process of claim 9, wherein (a) the cellulase-inducing carbohydrate is selected from the group consisting of cellulose, lactose, cellobiose, sophorose, gentiobiose, and a combination thereof; (b) the hemicellulose-derived carbohydrate is selected from the group consisting of xylan, arabinoxylan, xylo-oligosaccharides, arabinoxylo-oligosaccharides, D-xylose, xylobiose, L-arabinose, D-mannose, D-galactose, and combinations thereof; and (c) the non-inducing carbohydrate is selected from the group consisting of: glucose, dextrose, sucrose, molasses, fructose, glycerol, one or more organic acid, and any combination thereof.
 11. An isolated fungal cell capable of producing one or more biomass-degrading enzyme, comprising a decrease in copy number or expression, relative to a parental fungal cell from which the isolated fungal cell is derived, of a polynucleotide that hybridizes under at least high stringency conditions to any one of (i) the polypeptide coding sequence of SEQ ID NO; 2, (ii) a genomic DNA sequence comprising the polypeptide coding sequence of SEQ ID NO: 2, and (iii) a full-length complementary strand of (i) or (ii), wherein high stringency conditions are prehybridization and hybridization at 42° C. for 12 to 24 hours in 5×SSPE, 0.3% SD5, 200 μg/mL sheared and denatured salmon sperm DNA, and 50% formamide followed by post-hybridization washes of three times each for 15 minutes using 2×SSC, 0.2% SDS at 65° C., wherein the fungal cell, when cultured in a fed-batch or continuous culture fermentation provided with a feed solution comprising a carbon source, exhibits at least about a 50% increase in maximal specific productivity (q_(p)) relative to a parental fungal cell from which the isolated fungal cell is derived cultured under the same conditions. 